Why are the joysticks different?
Buttons look like they are spaced too far apart but maybe you like it that way.
uhm.... The Joysticks are the same type, but maybe you're seeing something I don't, I'm not too experienced at this, all I can tell you is that I purchased this Bartop Kit from a company online, and I believe you may be right, I had some questions myself, for example, the controller panel area was a pain to wire due to the limited work space, I couldn't even fit my hand with a screw driver to set up the Joysticks, this was because they sell you this cabinet fully assembled, which I think is great, but Glued?

? yes! it came Glued, and with screws.
The bottom Panel piece was glued also, which made it impossible to remove it, so yes, the wiring was a nightmare.
I wouldn't be surprised if the buttons are drilled by the standard technics but really, but overall, the kit is really nice.