Listening to Wheelocks pronunciation files the the reader pronounces words with -iam at the end of the word as “yam” but in words with -ius at the end the vowels are pronounced separately. Why wouldn’t words with -ius at the end be pronounced “yuhs” as in the word alius?
If he doesn’t pronounce filiam as three syllables, then he’s doing it incorrectly. Unless there is a vowel before the i (Troia), or unless it is at the beginning of the word, (iam), it shouldn’t be pronounced like a y.
Incidentally, even though iam is one syllable, etiam is three.