Is it possible to start season 3 with all routes active? If so how to do it?
Somewhat. It's not recommended by scrappy to do this, and he will be coming out with a newer version of the mod that does allow you to do this without major issues (eventually), but you can technically make it happen in the current state of the mod.Is it possible to stay with both the MG and the Side Girls with the mod in Season 3?
You just have to go into the mod menu, click the "Variables" tab, and then click each of the names of the main LIs and the last name on the list (I forget what it says but its something like "Other" or "Miscellaneous") and click the option that says "On {X} route" and all the options that correspond with dating them, and ignore the warning that says you should only be on one path. If you do that you will be able to do most of the side girl scenes and some of the main girl scenes, although there will still be some things you will miss, this is the best way to get the most content in a single playthrough.
I also recommend using a walkthrough while playing because some scenes check "if you are on {X} path then end relationship with {Y}", and you can avoid ending the relationship if you just turn off the path for the duration of that scene (or just when that check happens). And you should save often to ensure you don't fuck something up.
But like I said, if you're worried about major issues, you should probably wait for Scrappy to release the full version of the mod, as you will not be able to see every scene in one playthrough anyway. No one has any idea when that will come though.