A little more testing I've done as I don't spend a ton of time on emulators but I have found that AFMF seems to be working in OpenGL with PCSX2 so you can get your compatibility from using OpenGL and some benefits that AFMF provides.
As stated above you need to put PCSX2 in your AMD games list through the drivers, plus I have "Optimizations for windowed games" enabled on in windows. You have to double click the emulator while running the game to make it run in full screen (even though it is still borderless windowed) or use your hotkey to make that happen. Once you do those two things and have AFMF enabled through the drivers it should automatically be working, if it isn't you can always use your hotkey within AMD's drivers to enable AFMF.
I have tested AFMF running through OpenGL in only two games so far (Jak II and FFX), however both seem to work. That said Jak II really doesn't feel good while playing when AFMF is on so I turned it off. FFX running OpenGL seems to work fine however.
No idea how it is working but it seems to as keeping the AMD overlay on states I'm running at 120 FPS with Frame Gen Lag being correctly reported.
Edit: Duckstation running OpenGL does NOT seem to work the same way. Just tried to run Parasite Eve in OGL and AFMF will not enable. It gives the normal "Must be running DX11 or DX12" message. No idea why PCSX2 works and DS doesn't.
Version of PCSX2 used: v2.0.3