Well with regards to your points:
1) You actually route out LESS with a top mount, all you need to do is rout out to depth of the mounting plate. Yeah, you have to cut a whole to put the rest of joystick through, but the mounting bolts are actually going through a lot of wood. Its plenty sturdy, especially for non-comnercial use.
2) Well, maybe with the spacer, all the other stuff you can do from the bottom. Plus, like I said, in a home use situation, you probably won't be doing this all that often.
3) You have to route ANYWAY if you bottom mount, In fact you have to route a lot more since you have to route oute several CM to get the jostick at the right depth, and seriously? 1cm is a lot more routing then 2mm?
4) I would say its more like 50-50 in terms of what is designed for wood panel vs metal panel
That being said, I have nothing against bottom mounting, just wanted to point out that top mounting IS an option.