No, you do not necessarily need an extension for a JLW in a 1/4" - 3/8" panel. I have a JLW in a routed 5/8" panel (1/4" nominal thickness at mounting plate) and the stock lever/knob is just marginally shorter than my Ultimarc "long" MagStik balltop mounted in T-Stick Plus joysticks. I tried the JLW with an extension and it made the lever just a bit too tall imho.
I'm not 100% sure that MagStik levers are compatible with a JLW stick, but if Andy says so then it must be the case. Yes, the JLW stick (and the MagStik levers individually) come with dust washers.
You should be fine with the pushbutton length.
I think the MiniPac is likely packaged with its own PCB feet, but if you're using a wood panel it shouldn't matter much if you mounted it direct to wood.
Button wrenches are handy, but not 100% necessary. You can hand tighten the ring nuts and snug them with a pair of channellocks if you have to.