I think this is a fundamentally different kind of phenomenon. Historical sound changes that occurred between Middle Chinese and the present can explain why the same word is pronounced differently in different varieties of Chinese.
But they can't explain why or how certain people perceive different sounds to be equivalent. Consider a non-Chinese example - the letter Y in the English words yard and day derives from an original G. (There was also a G at the end of the word I, and it changed in the same way, but this is not reflected by a letter Y in the modern spelling of I.)
But the historical sound change does not mean that modern English speakers have trouble telling the difference between the sound of a Y and the sound of a G. They don't. All modern speakers will effortlessly maintain the distinction between yard and guard or gird, and between yes and guess, just like they maintain the distinctions between big and bee or bag and bay. If you suggested to them that any such pair of words might sound similar to each other, they'd give you funny looks.
I'm interested in the ability of speakers to produce and perceive differences between different sounds, not in the different evolution of one sound as it develops along different historical paths. (Well, not here. I am interested in the historical development of the sound as a more general matter, but it's not what I was asking about.)
I was hoping that a fuller understanding of the identification of r- and y- in certain Chinese regions might help explain why certain pinyin syllables are spelled with an initial letter Y. For example, I have been saying that "yue" represents the combination of a final -üe with a zero initial, and this is indeed the official definition, but there's a bit more to it than that - I knew a Cantonese girl for whom the Mandarin words 肉 and 月 began with the same sound. That's easy to explain if "yue" really does have an initial y-; it's much harder to explain if "yue" has no initial consonant.