Thanks! I don't have discord, but feel free to share your edits on any publicly available site if you want me to have a look (itch.io, google drive, etc.).
Not sure if an expanded version would fit in with in the main mod, limiting the main mod to only vanilla missions seems cleaner to me. But more random missions as content pack or optional expansion might work well.
1. I'm sadly not aware of a simple way to make the blend in happen while replacing the intro cutscene in a way that works with all locations on all missions. Removing the cutscene would be possible, but only doing it for some intros would likely be a lot of work, as the cutscene is tied to the random selection process.
2. Should be possible, not sure why I didn't include them before. That said, don't hold your breath. No idea if/when I find more time for modding.
3. For me personally, more than 4 is a bit much. At the moment I have no plans to work on that, but I think your idea might technically be possible: the number cannot be totally random, as the mission json needs to have a separate entry for each target, but it might be possible to disable a random number of those entries.