Hello. So I kept experimenting to find a solution. I tried different settings in BIOS etc. Nothing worked. Then I remembered my MB got 2 BIOS'. So I switched to 2nd (which was stock version 4602), enabled power on by PCIe in APM, shut down pc fully and tried waking it up as usual. And oh, magic happened and everything worked as it's supposed to.
I then proceeded to eliminate possibility of wrongly configured BIOS1 by reverting settings to defaults and even removing battery. Still didn’t work. At this point, it was obvious that the cause is within this revision of BIOS (4901). I then decided to flash lower revision of BIOS and see at which one it still works. I ended up with 4802, which last one before 4901.
Conclusion: If you encounter same problem with this MB, simply downgrade your BIOS to revision 4802, either via:
1. Use BIOS flashback (put needed .CAP onto flash drive, rename it to R4E.CAP, put flash stick into ROG connect usb port, hold ROG connect button for like 3 seconds )
2. If your BIOS2 revision < 4802, go to BIOS2->Tools->BIOS Flashback, select copy BIOS2 to BIOS1, then switch back to BIOS1 and upgrade it to 4802.
Hope this helps someone.