(a) I’m pretty sure the switches are going to end up slightly rotated, unless you bend (maybe just one of?) the pins on every switch to fit. It would be possible to make an alternate design where either Cherry MX or Alps switches would fit on the same PCB, but it would take at least a little bit of tweaking.
(b) The existing acrylic switch plate for the Ergodox (e.g. the one shipped by MassDrop) is not the right shape for Alps switches (and also thicker than ideal). You might have to make your own plate design
(c) You may have trouble with stabilizers if you decide to use 2x1 thumb keys: either your plate design will need to be quite thin with holes cut out for Alps-style stabilizers, or you’ll have to find keycaps with MX mounts for stabilizer inserts, and use Costar-style stabilizers; if you go for the costar-style stabs, you can source 2x1 keycaps (either DSA or DCS) from Signature Plastics.
If you actually want to go to the trouble of redesigning PCB + plate, I’d recommend changing the design quite a bit from the Ergodox. I think there are at least 3-4 low-hanging improvements to make.