1. I too am really disappointed by the lack of rebel troops! (and clone troopers as well (yes ik there's that ONE guy) but I digress) What you could do is use other enemies that have the same feel to them as rebel troops would. If you put the "rebels" on one team (orange) and the troopers on another (blue) then you as the hero could choose a color and then fight. You could still achieve what you want you just have to make "enemies" friendly by putting yourself on the same team as one of them.
I know you can do this with the enemy generators, not sure about the wave generators but probably: look at the generator's properties and set it so that it generates the "enemy" as a member of a specific team. Don't try to mess around with like dropping the enemies into the team color thing LOL (my brother did this in 1.0)
2. Having the playable rebels as NPC quest givers IS possible. You just have to use the townsperson figures. I use a townsperson + dynamic trigger + context button assigner + text creator + a camera to allow the players to talk with NPCs. (Dynamic Trigger is connected to a townsperson so that when the player approaches the townsperson the DT is "triggered" which makes the context button assigner activate making a button prompt appear. The player can then press the designated button and then this will trigger the text creator and the camera. The text creator will display the text while the camera will show the townsperson so that the player has that visual for who's talking even if every line of text begins with who's talking "Ezra: I like soup" "Zeb: I like soup more than you, rat"
3. Do you mean going from the planet's surface into space? You could have one toybox where you're on the planet's surface and then have some sort of fighter hangar where the player goes and then they have to do something to "ready their ship" and then whenever they're ready they can "travel into space" by being taken into another toybox via toybox door which will just be a space setting and have no ground other than maybe hologram blocks so that the player can get in their ship
There are limitations to the toybox and then there are perceived limitations to the toybox. Perceived limitations can be very physical things such as "I can't have different classes of clone troopers for my republic army!". There's only one "clone trooper" toy. However, there are storm troopers. There are jetpacked Mandalorians. The storm troopers are a natural evolution of the clone troopers. The clone trooper armor is Mandalorian in origin. You could use those as additional classes to your clones and simply ask the player to make a logical leap.
When I played Ezra's Spark of Rebellion (I haven't delved into Community Content much so this is like my one big experience LOL), I felt like I was on Lothal. Even though tons of non-star wars toys were being used to create it, everything felt like it was straight out of the show. I felt like I was in the Star Wars universe despite the fact that there were Agrabah toys and modern city toys all over. We aren't always as limited as we think we are.