Why are う and い used to prolong ~O and ~E, instead of お and え?


When was this rule to prolong short vowels added to Japanese?  
And is there any formally accepted reason for using う and い instead of お and
え? (which would seem like a more natural option, in my opinion)

There are examples where お is used after a syllable ending in ~O, are these
phonetically equivalent? とお(遠) and とう(塔)?

Edit: My question, specifically is why is う used to make syllables ending in O
long, when a more intuitive and natural option would have been using お (And
this premise is totally subjective and my opinion, if someone disagrees,
please explain)




Historically えい and おう were pronounced differently from ええ and おお, the first
two as diphthongs and the second as long vowels. Sound changes resulted in a
merger, but despite spelling reforms, the spellings remained separate.




Historically えい and おう were pronounced differently from ええ and おお, the first
two as diphthongs and the second as long vowels. Sound changes resulted in a
merger, but despite spelling reforms, the spellings remained separate.

