I was searching through the whole stroghold, also in spectator with night vision and can't find the portal...
Maybe it is a generating bug

I have also some other mods installed like repurposed structures and end remastered, could there be a problem with them?

Tbh I suspect you just haven't found it. But if you provide the seed, I can take a look.

nvm, found it now...
sorry for bothering you.

Lol no worries