It would be one thing if you have an AMV with an end credits sequence, but even then, the pop up boxes will obscure something that you put a lot of work into trying to make just right.
I really don't mean to call out anyone specific here, these are just a few examples and I hope they get my point across.

This video is less than 2 minutes long, yet the screen starts to get cluttered with this stuff starting at the 1:32 mark. That's 18% of the video's runtime with something big covering up 10% of the screen, with an additional 5-6% of the screen covered shortly afterward in the opposite corner.

This card pops up at the conclusion of the video in what's supposed to be an emotionally devastating climax. The moment is completely ruined! I'm really not sure that the editor of this video is aware of how this option on YouTube actually sabotages his work.
YouTube will never stop coming up with new ways to "engage" your viewers. You can say no to these and sometimes there's good reason to.