I'm likely going to try a Custom 3 soon myself. Based on various pickups I've put A3s in before, my expectation is it will be darker than the Custom Custom. So far every pickup I've swapped from A2 to A3 has ended up gaining a tiny bit of low end and losing quite a lot of high end, though I do always adjust the pickup height to compensate for the weaker magnet. I expect when people hear the A3 being thinner or brighter it's because they put it at the same height as the A2 pickup, so they get less output and that almost always translates into a brighter sound. If you raise the A3 pickup up a little so it matches the A2 in output, the A3 ends up being the darker of the two. (Again, at least in all the pickups I've tried it in so far, with the Custom 3 probably next.)
A4 and UOA5 are two I have tried in the Custom wind already. Very similar EQ to my ears and just a slight change in output (A4 was a tiny bit hotter when I tried that), small enough that I wouldn't bother favouring one over the other. The most noticeable difference is the A4 had ever-so-slightly sharper pick attack, while the UOA5 was a fraction softer in response. They both sound like the Custom 5 that has been evened out a little, with just a touch more mids and an equally small drop in bass and treble.
When I have a pickup that's just a little bit too dark or needs to open up a little bit (note: I've not done this with a Custom model yet, tends to be more for neck pickups), instead of swapping magnets I just wire in an additional resistor to one coil. The value depends on the pickup in question and exactly how much I need it to open up. Usually I wire up a pot as a 'spin-a-split', turn it until I get the amount of mismatching I want, then disconnect the pot and measure what kind of resistance it's at so I know what resistor to add. It's a bit of effort but it's worth it, as knocking down one coil just the right amount can really open up and brighten a pickup without significantly changing the overall EQ or output. SD use this themselves for the Invader neck model, which as standard has a small capacitor on one coil to make the coils more uneven.
If you could work out what value resistor you need to knock down one of the coils of the Custom Custom by 5-10%, I bet that would lift that darkness but you'd keep the mids you want.