Yup. My guess is that they didn't want whether or not you watch cutscenes to affect IGT since there are in-game rewards for meeting certain thresholds. They could have made cutscenes never count towards IGT, but meeting those thresholds might have been too easy. Just speculation though.
Cutscenes, even when skipped, will be counted towards IGT, but are not counted towards RTA. There is also the intro cutscene, which isn't "skipped" per se, but rather the game auto-saves after the intro and that save it what is used by runners when starting. If you go watch a run, you'll see the file selected for starting the run have 3:44 IGT already.
This has been the strategy for any% bowser amiibo categories since a week or two after launch. See https://www.speedrun.com/sm3dw_bf/run/zn1ex38m and https://www.speedrun.com/sm3dw_bfce/run/zp3wvqnm
Getting enough shines while Bowser is in Fury mode can skip a fight. You can do this without amiibo () but since you need Bowser to go into Fury 11 times, it's slower than getting 50 shines without amiibo. With amiibo, however, you can summon Bowser right before collecting a shine to get the same effect without the waiting, making 40 shines faster.
Amiibo is a thing now. Bowser Amiibo is on main page and all Amiibo is on CE page, along with itemless Bowser Amiibo.
In SM3DW Itemless, if you accidentally get an item you quit out of the level and retry. What is the equivalent for BF? Do you:
a ) get hit b ) die c ) load d ) something else
Would Bowser's Fury 2P make sense? I haven't gotten to mess around with it but I feel there may be some tech possible.