In theory, most stuff should work as it's 99% compatible, but there might well be something that breaks. Rather than symlinking it or some such, it's better to configure the necessary tools to use the pigz command instead and then you'll at least find out what works.

FWIW, I configure BackupPC to use pigz instead of gzip without any issues.

I've done that without issue in the past. It's argument compatible so never seemed to be a problem

Well, gzip works on extremely old .Z files too (compress).