If (IF) you will hit the rafters on all the brackets, then with small panels and low brackets a single screw per bracket will do.
Good luck locating the rafters. Stud finders, even the best and most expensive, don't see it under the rubber and 3/8" plywood, or give 1"-1.5" accuracy which is not good enough.
I tried to hit the rafters, but on some I missed them on purpose because there were already 3 or 4 closely spaced deck screws in that location, holding the plywood to rafter. With less than 1.5" between the screws sometimes. Talk about not driving more than 2 screws in rafter :)...
For locating those factory screws in plywood, you may use either rare earth magnet or any stud finder. Or just look closely and run your finger over it.
So you might have eventually to drive screws into the plywood near rafter. Now, to hold well in plywood, even with flat install and low bracket, you need more than one screw per bracket. Which should not be a problem if you space them 2.5"-3.0" apart. That's why you might need 6" long bracket 3" or 4" wide. And plenty of roof sealant under the bracket - it will both prevent the leakage and will help to hold the bracket. I also lubricated every screw with sealant before driving it in, and covered the screw heads with sealant.
Yes, 1/4" plywood (usually on aluminum top roofs, fiberglass or when block foam insulation is used) is different from EPDM over 3/8" plywood. The OP has EPDM over (probably) 3/8" ply. Which he'd better check before drilling.