This is just amazing and I'm so glad to see PPS embracing code updates/changes to older games. Soren has done great work in the past for free but making these changes is a daunting and time consuming task. He should definitely be reimbursed for his hard work.
I suspect that the code for these games has long since been lost (maybe some of the original programmers have them still. but they can't admit to that).
I agree that there needs to be a paid download option. Perhaps you get emailed a rom file would be the easiest solution? Assuming the files are small enough for email. Please buy from authorized places and don't pirate this work. I very much want to see this continue.
I believe a couple people have said they don't think MB will get changes because of MBr. The remake uses a rom and emulator under the hood so there's no reason they couldn't put out an update with an updated rom. I'm not really familiar with any bugs in AFM, MB or MM myself though so I don't know what could even be done for them.