So if I start working on my PM+BrawlEX build right now and new versions are released, I'm not going to lose my progress right?
I don't think so, but it depends on what exactly you update.
In terms of code changes, you'll just have to do what I do and save any changes you plan to make in a NEW RSBE01, and then fuse it to the RSBE01 that comes with PM+BEX.
In terms of cosmetic stuff, that depends on what is added in future updates, so you'll likely have to redo replacements and such with each new sc_selcharacter, sc_selmap, and so on.
Also, has anyone had any luck adding the Stage Expansion template to PM+BrawlEX?
I have had luck with this. Currently on 0.4 with maxed out SSS and almost every expansion slot filled, works like a charm as far as I can tell.