Hi,
I have many times problems with MSU patches that are in bps format if they want to be combined with other hacks, e.g., latest here where Vitor released a SA-1 patch for gradius (v17), but we only offer a msu support bps for v16:

https://www.zeldix.net/t1522p100-gradius-iii#42157

instead of giving the error message "This patch is not intended for this ROM." could you maybe make a warning instead alike:

"Warning: This patch is not intended for this ROM. Do you want to patch anyway?" And then let the user decide with Yes/No.

The command line :
flips --ignore-checksum --apply patch.bps rom.sfc
is already doing this, but having this option in the GUI would be a great advantage imo!