Nothing was disabled except for the 20+ mods that I had been using. Only the Wube's mods (Base, Quality, Elevated Rails, Recycler, Space Age) were enabled.
The answer to your second question is a rather simple answer that I discovered while playing around and testing out Factorio: To earn T3 qual modules and Legendary while still on Nauvis (but without using a mod), simply start the game without Space Age. Play until your base acquires those techs, then Save, then Exit and enable the Space Age mod, then load the Save game. Enabling the Space Age mod on a saved game will not take away techs that have already been discovered. Note, however, that I have not played a full game using this method. I tested this by starting a game, giving myself all techs (using a mod), then saving, then exiting and enabling Space Age and then reloading that save. I then looked at the tech tree.
I don't consider your mod to be bugged. It's not uncommon for some mods to not be compatible with others, and also not unheard of that some mods can cause strange effects when used on a Save game that has many hours in it.