A message from the author of RAD source port, who I had previously contacted on Doomworld forums.

Can you put a note somewhere in rules for E2M2, Episode 2 and/or Full Game that E2M2 requires only 2 out of 3 secrets for a valid 100% run?

That aside, the current category rules text state "100% completion" without specifying what it actually is. In all 100% speedruns I've done so far I went for 100% kills + 100% secrets + completed secondary objective.