Which is why TRACE - the biggest duplicator back in the day - did NOT (exceptions apply) do this. They asked customers to supply scripts in FreeForm. Here formats and protections were defined. The system exactly knew what was duped.
As you are unable to verify pure flux, most games had checksum data added.
It is correct that it's easy for a quick dupe, but you can't verify (unless you'd have parameters, but then that's not far from FreeForm), and copies in general come with generation loss. Since floppies are old and errors happen more frequently people should be aware of the issue.
Speaking of another format, I don't know of anything that could not be handled by ExtADF, IPF and maybe FDI. All of these are supported by WinUAE. The latter also has raw flux afaik.
But, why not surprise us and contribute to the WinUAE code base? Like we did with Vice when we pimped G64 support...