The shift in pronunciation wasn’t a simple and straightforward process. If you’re trying to argue that the reconstruction is faulty on the basis that the shift was >50% complete, I’d respond that nothing like that level of precision is possible. Moreover, I’d expect funerary songs to be a bit conservative in their pronunciation.
Even Modern Greek, despite the homogenization effect of modern communications, still has local dialects which sound very different from one another and aren't easily intelligible to speakers of the standard dialect.