I have never seen any ad on youtube; are they really integrated into the video itself ? from the fact that I never saw any either in the browser (with ublock origin) or through youtube-dl, I kinda just assumed they were distinct videos played by the JS player beforehand - and thus easy to bypass - and not an integral part of the main video file.

Anyway, to answer your question: youtube-dl can perform the page fetching and the download in the context of an authenticated user (for example for age-limited videos), so I assume that any advantages associated with a youtube account would most likely work with it.

I think in at least some cases they are integrated, because I use ublock origin as well and I did see at least some ads before I got YouTube Red. I could be wrong but that's my impression.

Hmm, you could well be right and I simply didn't watch the right videos.

It just doesn't download the ad at all. You can specifically tell it to try to download the ad, but just don't do that and you get ad-free, no matter if you have YouTube Red or not.