When an active-passive switch pops, technically the problem is with the preamp design, not the switch. The pop is usually an input or output coupling cap that doesn't have an earth reference. IOW, when the output or input is disconnected, it's floating, usually at 4.5V. Then when you connect a pickup or an output jack or whatever, it snaps to zero volts (earth) and creates the pop sound. The resistor that could bleed this voltage and keep that side of the cap at earth may have been overlooked in the design stage, because the preamp was never intended to be wired in a certain configuration. (I'm speaking in general here, and not specifically about aguilar products. I haven't installed one for a few years, so can't speak for the OP's particular pre.)
I can only imagine that the reason one push-pull pops and the other doesn't for a preamp with a floating coupling cap, is that one switch is make-before-break and the other isn't. Or the guy has old stock of one brand and the switch contacts needed cleaning. (Dirty contacts can also cause switch noise.)
As for using other value pots for an active preamp. I wouldn't recommend it, although you can't really hurt anything by trying I guess. If the obp3 is like most 3-band preamps with a 3-way baxandall wrapped around an opamp, then as long as the pots are linear and the same value, anything from 20K to 100k should work, although I'd think the centre frequencies might shift slightly, and the cut/boost range would also be effected. Again, just speaking generally here. An educated guess. Oh, and if you have a stacked treble and bass control, then you might have trouble finding a pot other than 50K that's linear anyway.