I realize that this is a very old question and you probably know the answer already, but I'll put it here just for reference.
The answer is actually very simple. Because prior to 1946, historical kana orthography was used for BOTH Modern Japanese AND Classical Japanese.
People who were reading Classical Japanese texts were reading Japanese spelled in the same way they spelled their words in the present. So, they read the Classical Japanese words in the same way with the same pronunciations as they read their Modern Japanese words. The sound shifts and changes we use to pronounce Classical Japanese in the present day are directly based off of the sound shifts pre-1946 people pronounced the Modern Japanese language with. Because up until the 1946 reform, the pronunciations and phonology changed but the orthography stayed the same. As けふ changed into きょう, the people started saying きょう yet they still wrote down けふ, all the way until 1946 until the kana spelling was reformed to directly match the modern phonology (with the exception of は -> わ / へ -> ゑ -> え / を -> お, which are the only remnants of the sound shifts people regularly read Modern Japanese in prior to 1946 that still exist in the language today).
Really up until the reform, nobody found them "weird sound shifts". It was just the way everyone in Japan read and wrote text, that everyone had to learn and everyone used naturally. People didn't really question it until around the time of the reforms. When you were writing [今日]{きょう}, you were writing [今日]{けふ}. 今日 was spelled けふ, and you just pronounced it as /kyou/. You didn't spell 今日 as きょう or きよう, it was けふ. People were educated in the historical kana orthography spellings as they learned how to read and write - because there was no "modern kana orthography" at the time; this would just be the way Japanese was read and written, with this set of sound changes. They would be taught to you as you learned how to read.
It's like how "tough" in English is pronounced like "touf" but we still spell it as "tough". The final "gh" is a remnant of a sound that is no longer pronounced in the word in the modern day, but it was once there, and is the way people have been spelling the word for centuries. You don't really question why it's spelled "tough" or label it as a "weird sound change", you just know it's pronounced "touf".
Historical kana orthography has stuck around for Classical Japanese but is no longer used for Modern Japanese after the 1946 reform. There hasn't really been an incentive to change the way Classical Japanese is pronounced; after the reform, people who studied Classical Japanese just pronounced the historical kana orthography used to write it the same way they always knew - the way they learned and pronounced Modern Japanese written it it with.
