End Remastered uses a custom block for the portal frame, and it messes up the end portal room if using YUNGs Better Strongholds. Is there any chance we might get compatibility between the two?

Nevermind, I am just an idiot. I did not think to try and right-clicking the eye already in the portal with those from End Remastered. I guess I also assumed that the portal frames would have to be the ones it adds, but that does not seem to be the case either. End portal works just fine.