Unfortunately, when you write a program that doesn't wrap output FASTAs, you have a bunch of people telling you off because SOME programs (cough bioperl cough) have hard limits on line length :)

Is BioPerl still standard, did people move to BioPython?

When I was shown BioPerl I was tempted to write a better, C++ version, but was overwhelmed by other university stuff and let it go.

You can use content-defined chunking to wrap at a predictable place so that compression still works.