I don't understand what you mean by "the magic phase knocks out most of the sanity checks".
I was talking about if your army is moving from A to C through B, and your enemy casts Call of Winds on B. The game currently already does some sort of additional check on movement orders, because your army stays in A instead of ending up in C (assuming the hawks take B).
As far as computation time is concerned, I'm just speculating, but re-doing the test for underwater entry based on globals and commander amphibious attribute is just order N where N is the number of commanders, and even 15000 is an extremely small number for any system built since 1980.
