Suspect this has long been sorted and I haven't had the need to create a ROM file, but a program like Lara can handle Loading Binary Files & Saving COM Files, which would remove the Headers & I think Lara can Save COM files anywhere in Memory & not just from 100h.
With Lara though, it was good to End Program just clear the BASIC from Memory and then go back into it & the program runs in the extra 64k when 128Kb is detected.