I haven't heard of a mix of EPDM and TPO, it's usually one or another. but who knows, maybe...
The membrane material will determine the choice of a sealant, and you do need a sealant under the bracket foot, no matter if it's a well nut or deck screw. Almost any sealant is compatible with EPDM. TPO - don't know.
Well nut Vs deck screw(s): with well nut you HAVE to miss the rafter. With deck screw you don't have to hit it, it will just be stronger if you do. I hit the rafters with deck screws on some brackets, and didn't on others, but with 5 screws per 6"x4" bracket foot it should stay put even without rafter. I think 3*#10 deck screws per bracket is the very minimum, if you expect any winds or if brackets are higher than 2".
I decided against well nuts not because it needs 1/2" hole - my 5 #10 screws is a lot of a hole too - but because I wanted stainless hardware, and because I don't believe in rubber lasting more than a few years in Mexican heat.
To justify 45A controller you will need at least 600W array, IMO.