As far as I know, Zhuyin fuhao, or Bopomofo, is the first system of phonetic symbols devised to aid to write Chinese phonology.
That was in 1910, so we could say very recent in the history of Chinese.
So I wonder if the way in that the phonemes, or sounds if you will, were grouped and assigned a symbol did in any way standardize the phonemes that were in use by Chinese.
I want to be clear, what I mean is, I can imagine that may be two or more characters that had slightly different phonemes or sounds and/or tones, were standardized with a single bopomofo or later Pinyin to make things simpler. Did this happen?
Because before any attempt to make a phonetic writing system, I'm not sure if everybody knew that two different characters that were later rendered with the exact same bopomofo, were in fact the same sound, or slighltly different sounds.
I mean, before bopomofo, there wasn't a standard way or a common phonetic base language to refer to when stating that two characters were pronounced the same, for example, I guess in that time you had to say 气 sounds just like 七 (ignoring tones) and now you can refer to Pinyin and say both are rendered qi thus referring to a common base. (just imagine that this characters sounded a little different, may be one closer to zhi and the other closer to chi to illustrate my point)
I'm not sure if I was clear, if not, please ask and I'll try to explain better.