The research shows that people cannot even hear the difference between sounds not represented by phonemes in their own language
Right, as far as it goes.
The interesting and difficult thing here is that た・ちゃ and さ・しゃ are distinguished -only- by the consonant portion of the mora.
しゃ is [ɕa], while さ is [sa].
The oddity of ち and し is not -just- an artifact of western ears. It would be literally impossible to distinguish さ from しゃ if the consonant portion were allophonic (ie., perceived to be the same consonant). That means native speakers are easily able to distinguish these consonant sounds.
The 'oddity' of つ and ふ, on the other hand, is just an artifact of western ears. There's no need to distinguish the consonant sounds from the rest of the row here and doing so is probably difficult for native speakers without training.
Now, みゃ・にゃ・きゃ all behave as most westerners (or at least English speakers) probably expect - there's an extra 'y'-like sound inserted between the consonant and the vowel.
Here's the real kicker though.
(Maybe you want to look at this chart and see if you can see it...
Hiragana - Wikipedia, the free encyclopedia )
That weirdness of ちゃ and しゃ? It -also- exists in the は行. ひ is not pronounced with the same consonant as は・へ・ほ, but ひゃ・ひゅ・ひょ are that consonant with the expected vowels. (That consonant being the
Voiceless palatal fricative - Wikipedia, the free encyclopedia )
This consonant mostly doesn't exist in English, but exists I believe in a few British accents. (Monty Python's Holy Grail comes to mind... 'ひゅ-ge ... tracts of land'.)
Any-way, I think は行 is an excellent object lesson in how a row can sound subjectively 'consistent' while actually -not- being consistent. At least, in my experience, English speakers always focus on the irrelevant ふ and do not notice that ひ stands out as an exception because it's close enough that we hear it as an 'h'-sound.
That subjective sense of consistency is probably similar to how native speakers feel about た行 and さ行.