Umm there is no semantic difference here. But istasyon is only used for railways and durak is used for rest of transportation( busses, metro, ferry)
İstasyon is obviously a loanword (station). Durak is Turkish.
The reason i think would be in the times of Ottoman Empire. Those times we had trains but no highways. In Ottoman era people didn't care about foreign word usage. Only after republic, with the establishment of Türk Dil Kurumu, we removed some foreign words and replaced them with forgotten Turkish words or new words created from original Turkish roots.
Durak is one of these new words. But sometimes people simply didn't stop using some of the removed words (they already had a word for train stations istasyon, they didn't switch to durak for them. But for busses. It was a new thing and for that, the usage of durak was promoted). There were cases of people didn't accept new words too. No one uses sepettopu for basketball.
So istasyon is one of these lingering words.