I'm not to good at 100%, but I'll put my 2 cents in every once in a while, usually for target tests and fights.
I'd definitely say the adventure mode timing should be the timing for both categories. Its much more accurate.
Just found this out, but the skip does actually negate the Web version from pretty much being faster in adventure mode. The function is not in the Web version for some reason, while the downloadable PC version does. Im still all for the skip being allowed, and still think its legal.
I used it due to it being a function in the games code. the skip function is there and has been there, so id say its a legal action to use when running the game.
I'm not sure if there would be more categories because of it (No Warps, Warps runs etc.), but since its in the games code, I feel like its usable.
How do you guys feel about the Ctrl+Enter button combination that skips levels? Should it be in its own separate category for runs, or should it be negated completely? Because Im not sure if its a cheat, or a exploit of what the game engine has.