For the first time ever I'm doing modded Morrowind playthrough(last time I played was probably was around 2010 when I was still a wee lad): Tamriel Rebuilt, Skyrim Home of the Nords, Project Cyrodil all that jazz that adds Morrowind mainland and several places beyond the borders plus whathever mods are needed for it to run and some "modernization" mods that are mostly QoL type of stuff(making picked up plants dissapear and so on, no always hit mod) and slower levelling.
Back to the question at hand though: Does the glitchy way of joining both Telvani and Hlaalu from vanilla Morrowind would still alow me to do the Hlaalu content in the mod(for example Narsis storyline against the sload drug-cartel)? Google AI suggests it'd work but I'd rather got an answer from actual people. The old way, as far as I know allowed you to join Hlaalu even if you already was a member of another house. My fav, due to being magic focused(and murder since they are a bit unhinged) were always Telvanni. Telvanni in vanilla were more interesting to me and I wouldn't want to miss out that this playthrough(I basically plan to pretty much visit all the modded expansions after wrapping up main story in Morrowind, Anvil and Narsis especially).
Other factions and guilds apart from the Great Houses, I'm led to believe, have their separated chapters outside the vanilla Morrowind and don't clash even if I were to become a persona non-grata of, let's say Fighters Guild in the vanilla locations.