I created a second account and so far I've not gotten that popup, but then again, it hasn't appeared in recent days when I use my old account either. So yeah, YT is definitely experimenting, trying to find the best way to make our experience difficult.
Freetube is missing some useful features.
But I continue to generally use youtube.com to search or manage lists and then copy the links of videos I want to watch to Freetube.
Also, I am gradually moving my YT subscriptions to freetube as I go so finding stuff I want to watch on FT is gradually getting easier.
Though eventually Google will probably restrict API access rendering some alternatives useless.