A little late to the party on this discussion, but I thought I'd chime in. While helping TAS Mario 2, Aglar and I came across the Mouser skip and I personally did some testing to see whether it would save time in the end (it did not). There was some discussion among other SMB2 TASers on this topic and the consensus was that it shouldn't count as "all levels" if the Mouser skip was going to be used. It didn't matter in the end because it was very slightly slower, but this was a thought given how close the routes were time-wise.
Ultimately, I think it doesn't make a whole lot of sense to track something as "all levels" when you're warping from one stage to another (seamlessly, but still). In the case of the other "wrong warps," it's in-stage and I think should be viable. The problem I see if simply that with the Mouser skip, all levels aren't actually being completed, although 1-2 is visited, 1-2 is bypassed.
interesting. i thought that wiuld result in grabbing the flag. i'l have to test that out.