Okay, after blowing up #bizhawk, a useable script was made.
https://pastebin.com/EhS6Tg3x
Here's what I found by watching the movies with this activated.
When the Boardin' Zone 2 mine dropper doesn't spawn, we manage to have the camera pass through the center of the vertical spawn zone, above the horizontal spawn zone, and then pass through the center of the horizontal spawn zone going down.
In stage three, the first time he shows up, the camera just barely passes through the top pixel of his spawn zone. Sadly, it looks like the camera is at its top height at that point, so unless we can figure out a way to push the camera just a little bit higher, it's probably a "no" for despawning him there.
As for the second time, it's probably a "no" as well, but I'll definitely play around with it.
EDIT: wrong link in post. fixed link.