I hope this isn't too disappointing: There are no significant
differences between this R-Type prototype and the final build.

One minor difference is that the prototype's header region contains only
$ff bytes. The final build adds "TMR SEGA", a checksum, a product code
(although the byte containing the high nibble and version number remains
$ff) and a region code & ROM size.

All of the other differences occur at the end of banks - specifically
banks 2, 5, 6, 7, 8, 9, 11, 14, 15, 20 and 31. In each case, the
prototype contains $ff bytes as padding. Although the final build
appears to use this space for additional data, in fact it simply
contains different padding - the data corresponds exactly with the bytes
from the previous bank (or, in the case of bank 2, the bytes from bank
31).

Thanks

Paul