So I installed the Mods as Community Portal provided in order and seemed to work fine because this time I did not get the cutscene in the same place as before. Plus before I wasn't even getting the Nihilus cutscene only the damaged ship in the space and when it shifts to Visas it crashed.
But now I'm getting the cutscenes IN the Hawk before even landing in Telos after I finish my conversation with Kreia(Must be alignment you mentioned before).
Problem now is that after the Darth Nihilus cutscene in the Ebon Hawk, I'm getting the Atton-T3 conversation and then Kreia comes and incapacitates T3. But afterwards nothing is changed everything is fine. I don't get any unique dialogue of what happened.