The pronunciation may not be perfect; however, it is the best pronunciation we have for Homeric Verse and other Ancient Poets. The Modern or Koine Pronunciation simply does not work with them; but though his vowel pronunciations have some credibility on that account, consonants are more difficult to judge as they must be measured using less certain linguistic rules.
I do not see how this creates a discrepancy in the evolution of the Greek language, vowel and other pronunciation shifts are found in every language. Grimm's Law is applicable to Indo-European Language be it English, German, Russian, Latin, Persian, Sanskirt, or Greek; and concerning vowel shifts, there is evidence for at least two great vowel shifts (as well as numerous minor one) in English since the norman conquest (not counting the radical linguistic upheval of that period and the next couple centuries). The first was between Chaucer and Modern English, towards the end of the Middle English Era, and the Other has occured within the Modern English Era.