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Not sure what what your point is here. ず＆づ may or may not be phonetically indistinct based on region.In Standard Japanese orthography, all occurrences of <づ> have been replaced with <ず> except where structural reasons remain; the etymology is irrelevant for the orthography and so is the pronunciation in different dialects. In dialects that maintain the distinction between them, many instances of <ず> are pronounced as <づ>, and dialects in general do not follow the standard structure and grammar.
It is absolutely not the case that some actual spoken dialect of Japanese exists somewhere that follows the distinction between them as written in standard Japanese.
> I guess my original point was that just because you can type certain kana in different ways that may not be strictly phonetic they make sense as simplifications based on the structures you mention, and they make typing easier.
They do, but the input method is not based on phonology but on structure and Japanese orthography which does not strictly follow the phonoogy of Japanese.
My point is that it is not entered how it is pronounced in Japanese, but that word in Japanese has an official hiragana speling, which may or may not correspond with how it actually is pronounced, and a system that neatly maps to that spelling is used to enter the characters, not the pronunciation of it.
The official hiragana spelling of such words came before the invention of i.m.e.'s.
> This does not mean you cannot type using inputs that correspond to more strictly phonetic romanizations e.g. hepburn.
I do not subscribe to the theory that Hepburn is more phonetic or phonemic than Kunrei myself; <hu> seems to be a closer approximation for modern Japanse than <fu> in particular than <tyu>, as in “tube” also corresponds better than <chu> as in “chew” to me.
Having said that, that's harder because Hepburn is lossy with regards to the original hiragana orthography and neutralizes <づ> and <ず> among some others.