The loading speed of the MEGA65 from a D81-Image is blazing fast: if you read a file that span the whole disk just using kernel routines, it will take about 15 seconds.
Only cause for using Jiffy would be "legacy" hardware like a 1541, mostly for "migrating software". For 3.5" floppies would will most probably use the internal drive, SD-card readers like the Atmega based ones are rather pointless, because the MEGA65 is also planned to have SD card support.
Imho, a good solution would be either a community-patched kernel or a program that patches the kernel during runtime. I'd also suggest to go for an open source reimplementation of the JiffyDOS serial line protocol, because of the copyright.
Also note, that the internal floppy would not benefit from any *DOS floppy speeder, as it is not connected via a bus (serial or other), but running as a different configuration of the C65 CPU. I also remember reading a statement of one of the engineers of the C65 that the floppy is rather slow due to that design and that there's not much room for improvement.