Have you scoped the local resale market? With mass-produced instruments like Fender that's where the value is IMO as long as you are diligent at making sure the instrument is in good shape before you buy...
Squier CV instruments can be absolutely killer for the money. Duds make it out there often enough at that price point, but since you have local stores that stock them you can try a few before you buy (or order from a shop that is good with returns)- make sure to check for neck straightness, twists, see that the truss rod nut moves, fret buzz, etc. One thing with them apart from occasional (often neck-related) quality-control issues is the weight can vary significantly- as much as 2-3 pounds for the same model. For the price, if you get a good example you can upgrade the electronics (I'd definitely upgrade the pots and jack, pickup is subjective as the stock ones sound good IMO), tuners (stock Squier tuners are never great, though they hold tune), and a custom paint job if you need to for less than a JMJ bass.
Of course what you get at that JMJ price apart from better resale value is nicer hardware (though you weren't impressed with the Hipshots), potentially nicer neck (subjective- many love the JMJ neck profile including myself, while the CV is more slim/svelte), maybe a better pickup (you said you couldn't notice much difference, it is somewhat subtle), cooler finish (you didn't like the relic thing, so that value would be lost on you). The Vintera II basses are very popular- I haven't had a chance to try one yet, but the arm contour on the body is a nice touch that none of the other new Mustangs have, nice finishes, apparently nice necks, etc.
The JMJ pickup won't be a direct drop-in on a CV bass without modding or swapping the pick guard as there are two different Mustang pickup lengths and the JMJ uses the larger one while the Squiers and Fender Vintera use the more common (and vintage-correct) smaller one (I believe the pole piece spacing of the JMJ is wider as well underneath the cover- there is only a single pole per string so this is actually pretty consequential on a Mustang pickup for string balance- read below on my experience). I wouldn't necessarily say the JMJ pickup is "better" sounding than the Squier pickup though- it is definitely wound hotter and so can tend to have a more aggressive output and midrange. The CV pickup is probably closer to a vintage Mustang pickup, both in the authentic size and winding specs. There are other aftermarket Mustang pickups to consider if you want to try something new that will be direct drop-in replacements in a CV Mustang, including the Nordstrand which has split poles per string like a P-bass and gets good reviews.
FWIW- my current Mustang is a mongrel consisting of an Olympic White CV Squier body (a particularly lightweight example I scored in the classifieds on TB, the whole bass is under 7 pounds), the CV bridge, a vintage Fender Musicmaster neck, Gotoh Reso-lite tuners, a JMJ pickguard and pickup, and some Hipshot barrel saddles to match up the string spacing with the pickup (with the CV bridge and JMJ pickup I had issues with a quiet E string til I was able to widen the spacing with the new saddles). The JMJ pickup is definitely growlier to my ears to the stock CV when I've compared them, but also a bit darker. I prefer the JMJ but could easily match them with some EQ