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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)
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2017-03-03T20:02:35.960
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2017-03-06T16:08:16.890
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question
orthography long-vowels
Why are う and い used to prolong ~O and ~E, instead of お and え?
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.
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2017-03-03T20:17:48.013
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2017-03-03T20:17:48.013
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answer