Yes, the ideal solution is that unless the mapper has an explicit control conflict with nametables, use the mirroring bit verbatim. This also means you have to header your ROMs correctly.
Though in this particular case, I think this is just the practical problem that the emulator author doesn't have control of what headers are out there. This is a single game mapper, and its header is wrong in the available version. There's no board variants. Even if there were ROMhacks, they would need the same mirroring anyway.
I assume zeromus felt it was more important to just let people run the one ROM that actually exists that people have and actually want to run, rather than having to run support for everyone who doesn't know how to fix a header. (Opionions differ; I'm sure byuu would have just told people to go fix their header.)
...or the "but what if I want to homebrew this mapper with a different mirroring" request: not actually a meaningful problem until someone puts their money where their mouth is and has something real they want to run.
So, yes in the ideal case it shouldn't, but in the real case that we have...
who cares?