Volume/volume vs. master volume/blend is really a matter of personal preference. There already a few threads on the topic in this forum.

Personally, I have vol/blend in my PJ--not by my design, that's just how the bass was built. The general consensus is that vol/vol is slightly "brighter" than vol/blend, and there are some bad blend pots on the market, so you have to choose carefully. I am not sure why you think it is "limiting" though--both setups are capable of the same range of sounds, so it's really a matter of preference.
Assuming you don't add any holes to the pickguard, my vote is vol/vol or vol/blend in your case. You could also go with stacked knobs if it's important for you to have a tone control on the bass. I am assuming you are comfortable with the woodworking to route for the J pickup.
