Thanks for pointing this out. I first learned about PerlIO::gzip years ago (early days of perl 5.8), and wasn't aware of PerlIO::via:gzip until now. (In general, I've used PerlIO::gzip as a convenience for reading compressed data -- not for writing -- and I've never seen any trouble, but given what the author said, it makes sense to switch.)
I too have used PerlIO::gzip for a number of years on many millions of files without ever seeing any sign of problems and none of the reported bugs affect me. But nobody has yet said that they've even used PerlIO::via::gzip, so my practical experience kind of balances out the author's noble warning, leaving me still uncertain.