I think you should be fine. just make sure you keep audio to the rest and you should be fine
The rules require you to have audio for all the run.
It can't be helped if YouTube decides to mute the audio. The only solutions to that are move to a different video sharing platform, have a music mod with non-copyrighted music, or for the mods to have a special circumstance for these songs.
I dont agree with just muting out long parts of the run. I havent seen youtube mute out parts itself and yeah you can use music mods
iirc you can replace songs when it finds copyrighted music and it mutes the audio until you do that so that does exist.
About a month ago, there was a community poll held in the discord to add IGT to Deltarune. After a close poll of about 70 to 5, we have added the use of IGT to the game. This IGT only makes a difference to the All Chapters categories, removing the time spent switching between chapter 1 and chapter 2