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J basses that are fully functional BOTH as passive as active AND passive

TL;DR Looking for J fiver that works well in passive mode and the pre is more like the icing on the cake than the cake itself.

I'm wondering, what basses or preamps are out there (or are there any) that are designed for the player who wants to run the bass in passive mode most of the time and then add in the active control in a way that integrates with the existing passive sound well. I think ideally it would allow for the same pickup blending options on a standard j (esp since I like adding the series/parallel mod), and would be easy to set flat with no boost compared with passive (another thing that's tricky with the john east) and then tone shape from there.

Sire V3 (budget, Asian mahogany body, $450-ish) or V7 (better build, alder or ash, $700-ish). Available in five-string, and Sire's preamp is designed for full function in passive mode, with volume, blend and master tone separate from the 3-band semi-para EQ. Volume jump between modes depends on how much you're boosting with the preamp; flat, there is zero level difference. There are quite a few guys singing Sire's praises on these boards, and they're not wrong; at like pricepoints, they're very hard to beat on feature set and quality.
 
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Personally, with passive blends, I don't hear any difference between where it is centered and where the bridge or neck starts and it is all bridge or neck. I've seen people say they do neck and 10% bridge, but I don't hear any difference between that and 0% bridge. The J-Retro has an active blend which gives you all of the nuances because it's doing the blend as an audio mixer would. That's the reason that there is no passive blend in passive mode, but the switch give you most of the options you would want. Audere has an active blend and that's the only other active blend that I know of. I'm sure there are others. Check to see if you can find a plate for the DJ5 before you embark on anything. The DJ-Retro has been back ordered for ever due to lack of availability of the slightly curved plate used on the DJ basses.

If you have a chance - take your passive bass, go full neck and add in 10% bridge. Now take a scredriver or something else that is metallic and tap the neck pickup polepieces lightly. Be careful to not touch the strings, not because it will kill anything, but will give you a small click that will be heard by whichever pickup is on. Now tap the bridge pickup. Do you get a click that comes through your amp? Bump it up to 90%. Do you get a click now? Now finally when the blend is centered or the dual volumes are equal, now you'll get a click.
 
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What is the output like, compared with a passive bass?
One of the big things I like about the Audere – it doesn’t have the high boost typical in other active basses. The Classic's (fixed) output is in the range of what a passive bass would be (unless, obviously, you were to boost the all the tone controls;)) The “Jazz” series output is adjustable, so you can match the output of another passive bass.
Do pedals respond the same way

I don’t use much for “effect” pedals, but do use a compressor and occasionally a VT DI – so that’s (one reason) why I like the output levels to be close when possible on the various basses.

I haven't had experience with other Preamps - just haven't had the need - but your description fits;
for the player who wants to run the bass in passive mode most of the time and then add in the active control in a way that integrates with the existing passive sound well

Just a thought: The Auderes are very reasonable priced, quick to install, and they don't seem to last long on the TB classifieds – so you wouldn’t be risking much if you were to give one a try…
(you'll have to do your own research as to which will fit into your bass)
 
That is one of the reasons that my old Peavey Dyna Bass Five is still my go to bass after all these years, as a passive bass those Super Ferrite pickups have the low and low mid punch to sit well in a mix and plenty of highs to cut through but can easily be tamed. In active mode the three bands are perfectly placed to control the specific needs of cut and boost to enhance the bass in any mix. Over the years I have tried a lot of the competition including most of those named previously and I decided to stand with my trusty old white Peavey.
 
I use a John East J-Tone and it's fantastic. I dialed in the overall gain, the bass/treble frequencies, and set the tone cap I wanted. If you set the gain carefully there won't be much difference between active and passive, and when in passive it works just like you'd expect a Vol/Vol/Tone Jazz bass setup to work.
 
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Pretty sure my dj5 didn’t have a John East setup but I did install one in my jazz bass. It sounded so good it made me stay active all the time. I opted for the passive tone control and added a jack plate in the typical side position.
 
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The John East really doesn't seemed designed for that, tho. It seems like the philosophy is, passive is there as a backup if you absolutely need it or if you have a picky engineer in the studio but otherwise it seems to me like the idea is that most users will leave the pre engaged most of the time. Like, for instance, in passive mode, you can't solo the neck pickup, you either get a 50/50 blend of the two pickups or full bridge. Blah that doesn't work for me, neck soloed is my favorite j bass setting.

As others have mentioned, the East uni pre has a passive tone control, and the balance works just as well in passive or active. I love mine. Although I do prefer the active mode, I use passive mode at least 30% of the time. I can't speak for the J-Retro deluxe drop in pre (I don't own one) but they too have a passive tone control.
 
I have a Longhorn Jazz bass that is an stock active bass with Kubicki preamp, it comes with a 4 way switch, off, active mid bump, active and passive. I added a set of DiMarzio Area J pickups, I think it sounds great and has all the options you mentioned.
 
You can get the Sadowsky preamp with a passive tone control (what Sadowsky calls “VTC” - or “Vintage Tone Control”) in addition to the regular active bass and treble boosts. The VTC can be used in both passive and active mode. This is what I have in my Lull M5V and it works great.
There are other preamps that do this, but the Sadowsky with VTC is exactly what the OP is describing.
 
The majority of preamps can be configured this way. Most active preamps just take your passively blended pickup signal (either from a blend control or from a volume/volume) and run it through an active EQ afterwards, so it is easy to simply bypass the preamp section with a switch and you still have your passive controls. Some of them run directly into a volume pot at the end, so if you use dual volumes as your blending mechanism you can just use the Master Volume as your “preamp volume”, since it will be bypassed with the preamp (just requires some extra control space).
The reason a few preamps (like yours) aren’t capable of this is because they incorporate active pickup blending, so the blending mechanism is part of the preamp itself. Frankly, for me the active buffered blending is one of the main perks of running an onboard preamp, as you are able to eliminate the effects of passive loading on your pickups and get clear tones that aren’t otherwise possible (active pickups do the same). If I just wanted an EQ I’d personally put it on my pedalboard where there is ample space and power to use lots of options beyond the limitations of an onboard EQ.

Some EMG pres would work for you that haven’t been mentioned yet: The EMG BQC is a three band on two stacked controls that can be setup like you want, or the EMG BTS if you don’t need the mid band (just stacked Bass/Treble), or VMC if you only want a sweepable mid (actually quite useful IMO for a 1-knob control).

The Aguilar OBP-1 is the preamp behind the Sadowsky pre, and can sometimes be found much cheaper (not sure what if anything Sadowsky changed in his version). They are quite limited though, boost-only for Bass and Treble and tend to raise the volume quite a bit when dialed in (up to 18db boost on both bands). The volume/tone with both knobs turned down is decently close to your input tone...