Thanks to the hints of Sage and karri now I understand the two loaders and the encryption, so I'm able to decrypt / encrrypt the two loaders.
For the OP, I have a basic patch to show only one of the two games (that requires more work to have a perfect result).
Assuming there is only one type of rom around, here is what you need to do.
First the second loader needs to be patched to remove the checksum control changing the hillighted values:
in the red ones:
than it's possible to change one of the game entrypoint to the value of the other, so that always the same game is loaded:
AD 26 is for Missile Command and 85 27 for super Asteroids.
What is missing from this patch:
1) the splashscren is unchanged and shows both the titles, it's possible to skip the splashscreen or change the image with another.
2) in the main title pressing left/right still try to change the title, but it loads always the same. This makes restarting the intro. The check for left/right directions should be disabled (yesterday night found the point where to patch it but can't remember it today and don't have time now to trace again te code)
3) the starting intro music is always that of missile command, but left/right changes it (that's a nice feature IMHO). Disabling the left/right check the Asteroids version will require to change the music to load on start.
All this things are not difficult, but time consuming, so I think I'll stop here.