> I also like having a single feed with new vids from every channel I’m subscribed to on invidious which I don’t think is possible on YouTube

That seems contrary to the idea that your RSS reader should be the one place you control your subscriptions from.

Which is something of a general problem—an on-site list of subscriptions is certainly also useful in ways the reader can’t really replicate in a generic way, yet it’s in the user’s interest to be the only one in control of that list instead of involving the website in it.

I can’t think of a good way to deal with this.

I can see the appeal of having a full feed RSS so you don't subscribe in two places, But I don't login and only use the RSS feeds. I use TT-RSS and just do subfolders for my feeds. If I click the Youtube folder it displays all the youtube feeds in order but I still have the option to drill down per channel.