If you want to change what ROMs you can distribute to, you can just change the strings it checks against to use any rom:
Note the AXVJ and AXPJ. Changing those to the game you want will fix it. Or changing the 2 "BEQ loc_201E410" to "B loc_201E410" will make it work no matter what game you use. To make those work, change "23 D0" @ 201E3C6 to 23 E0 and "1C D0" @201E3D4 to 1C E0. You really only need to change the first one, but might as well be thorough.
I'm not sure why you would want to make the ROM run without a master. How would you get it to write to a GBA cart if you had to have a flashcart in to launch the mb ROM or.. something..?
Also, something to think about regarding moving the mb ROMs between master GBA distro cart ROMs:
Each GBA distro cart has its own set of global variables it writes to in IWRAM(0x3000000-0x3008000). The mb ROMs use matching global variables in order to "inherit" data from the master cart. Things like seeding the RNG are done in all the distros in that way. The multiboot ROMs don't make their own RNG seed, they just get it from their master. Take this example:
3 multiboot ROMs, 3 different RNG locations. That's just an example, all the variables are like that in each one. So if you move a mb ROM from one distro cart to another distro cart, the resulting pokes you get may not be "legit" since they may not normally be able to exist since the mb ROM may read and use incorrect data from an IWRAM location that is incorrect. I think you mentioned that you got a lot of identical(almost identical?) Jirachis when you moved a distro ROM to a different cart in order to generate them and that may be why. They may not be "real" Jirachis that could have been generated at the original event.
The oldest ROM, sample0519, gets more data from the master distro cart than any of the others. Things like OT name and gender seem to be passed to it via IWRAM, not determined via RNG in the mb ROM. There's probably other data done the same way but I haven't looked. Really the only way to figure that stuff out would be to have the original Negaiboshi(sp?) distro ROM to look at.