I think the use of a 1541 or 1571 with a Mega65 would be a lot broader than just "migrating software". Modifying C64 software with C65 functionality accessible from C64 mode will be the most economical way to get some software library that uses the Mega65. Adding some features is not much work for the community and can be done with a limited size community. However, eliminating all 1541 dependencies from such software would be a lot of work. Therefore I think it is safe to expect many people will not go that route and simply connect a 1541 or 1571, problem solved, use the built-in floppy for software with no floppy assumptions.
Therefore I would expect that 5.25 floppy drives will be part of a common use-case with the Mega65 and this declaring them as "legacy" would not be justified. Therefore the desire for people to use fastload solutions like JiffyDOS looks justified to me and considering community activity around JiffyDOS I wouldn't be surprised if a Mega65 version would be developed.
Nobody knows wether the C65 supports the burst mode of the 1571?