Going from active to passive, need ideas for the five holes in my top

Go to an auto shop and ask for body panel filler plugs. They're typically black, but you could paint them to match. Simple fix and easily reversible.
 
Personally, I'd just put in a bypass switch. I tend to record passive, and gig active.

As for the "producer knob" thing. FWIW, a lot of studios have racks of stuff that lights up, but isn't even patched in. It's there to impress clients. The producer can reach over and tweak any number of knobs to appease a back-seat-driver... :D
 
For a 5 hole Jazz, I'd do Vol-Vol-Passive Treble-Passive Bass and Series/parallel switch. Only doing the passive bass/treble because there is an extra hole for it. I don't feel passive J's absolutely need bass cut.