Hey! To make the 'packed' version we followed the steps to build RetroArch from source using MSYS2. For many reasons we'd have preferred to use a standalone GBA emulator, but they're all missing dynamic rate control which is crucial for a smooth 60fps experience.
The goal was then to get it as small as possible (RA is usually hundreds of MB). Looking at the available ./configure options there's a ton of features that can be disabled. We also changed the app icon and removed any theme assets that weren't needed.
RA likes to create folders and update config on the fly, so I'd recommend to commit the whole tree to a git repo before running, so you can easily see what's changed and remove the junk before zipping it up.
Finally, the launcher is just a simple Win32 program made with wnim, which copies the correct ROM for your language and launches the game like so:
retroarch.exe -L path/to/mgba_libretro.dll goodboy.gba
With regards to Steam, I'm aware of other emulated titles being sold (e.g. Iridion II), so I'd be surprised if a game running in RetroArch was rejected, but couldn't say for certain.