Well, the Megaswitch isn't like a typical Fender switch - it's designed to do one specific thing. That's why they make 3 different 5-way Megaswitches to do different things, rather than 1 switch with multiple wiring options.
I think you have the "P" model Megaswitch, which uses the full HB in positions 1 & 5, the inner coils in position 2 and the outer coils in positions 3 & 4?
If you disconnect your coil-split wires (green/white) from the Megaswitch and instead have them going to a push-pull, the push-pull will switch off one coil (and always the same coil) when it's operated. Then I think you'd potentially get no signal in certain positions on the switch with the push-pull activated. Or maybe not, I can't pretend to totally understand how the switch works.
If you had individual push-pulls for the two pickups, then you could possibly do whatever you want, but it would be complicated. It's probably a case of trial and error to see what works.
I think if you want more "control" over how and when the humbuckers are split, you'd be better off with push-pulls and a standard 3-way Tele-style switch. Or maybe you could get the wiring you want with a double-wafer "super" switch.