The second paragraph can be answered in large part by What changes are made to the pronunciation of gairaigo? and by Less-approximate and more-approximate forms of loan words and by Different transcriptions for words with related origin .
As for the third paragraph, Wikipedia says the Agency for Cultural Affairs (文化庁) at the Ministry of Education of Japan (文部科学省) plays a role in language regulation. I don't know whether it influences spelling of words. I know that it deprecated hentaigana and certain kanji.
