no the save setting isn't the problem at all ^^
i'm pretty sure it's possible, but i don't know how the org. os is storing the information to what rom/save filename to write after reset.
this should be an important information beside the save setting, too.

ORG-OS -> ALT64 -> reset -> ORG-OS
-> ORG-OS: sets save type in fpga and stores romname where?
-> ALT64 overrides save type in fpga, stores romname in "/ED64/LASTROM.CFG"
-> ORG-OS reads save setting from fpga and romname from somewhere.
-> ORG-OS saves to the filename of the ALT64 rom.
so you have to find the place where the original os stores the rom filename and alter it in your cheating app, too.