Yes, it has the stock pickups.
I played it Sunday at church. It played great (and looked good too

). It sits in a different spot in the mix than my 5594...all the bright overtones put it more in the mix than underneath it. Some of that I'm sure is the brand new strings.
I like that the boost and cut of the treble knob work on different frequencies. Dialing back the treble warms up the tone but there's no mud or loss of definition. Definitely a different vibe than a passive tone control. Turning the treble up a bit brings on the "spank".
The mid sweep is very useful. I much prefer mid sweeps to preset frequencies. It's much easier to find and cut problem frequencies. Or to boost something a bit to change the character of the tone.
The bass knob and function will take a bit of getting used to. As I understand it, the J retro has a small built in bass boost and the knob is boost only. So fully counter clockwise basically is the least boosted bass. It sounds good, but I
think I would prefer no boost when the knob is fully counter clockwise just to have that option on board. It may also just require a slight technique change....on my Roadworn Jazz bass I get a great barky sound by soloing the neck pickup and plucking hard right over it. Moving towards the neck smooths out the bark and gets really mellow. If I do that on the 5560 it gets to be almost too much low end content (is too much bass a real thing?

), but soloing the neck pickup and plucking over the bridge pickup instead is better.
The thing I miss most is a pickup blend in passive mode. But I think the passive mode is intended more of as a "get out of trouble" option than to be a fully functional passive mode. In that case the switch between both pickups or bridge only makes sense...easy switching between two good sounds from a passive J bass.
Overall, I think I like it....it turns the 5560 into a really versatile "super J bass". A J bass purist may not enjoy the color that the J retro adds, but it does bring some interesting and useful features to the table. Maybe someday if I'm bored I'll put in the stock VVT plate and record the differences.