Not baffling at all (Kyoto vs Tokyo)
English speakers often have trouble with phonemes in some word position but not others. For example, may take some practice to be able to say "tsar" even though they have no trouble at all with "cats" << the "ts" sound often occurs in the middle and at the end of English words but there is no English word that starts with
The initial sound in Kyoto exists as an initial sound in words like cute, and ditto for by in byoyomi (cf. beauty) so it probably the spelling that throws people, not the phonemes. AS to Tokyo, I can't readily think of other words with kio in them but there are words like audio and radio. However, there is the example of Ohio that could be followed, especially as its also a placename. But there are two other factors thta should militate towrds pronouncing Kyoto and Tokyo in similar fashion. ONe is that they are both place names often coupled together, and the other is that Kyoto has often been mentioned in news bulletins in connection with the Kyoto Protocol, and there it is almost always pronounved correctly.
We do have aword in 3nglish that begins with ts and I haven't heard anyone have trouble with it - tsunami, now common also as a metaphor. Going back further, I can't recall any English speaking chess players have trouble with Zugzwang but as that is spelt with a zed I can easily imagine some people using the zed for that reason.
It's true that English has borrowed very many words from other languages, but mots of that occurred centuries ago, and asking a new go player to take on board dozens of Japanese terms in one fell swoop with little context or use in wider contexts is a big ask.
Incidentally, Japanese is probably even more receptive to loan words than English. Major sources are chinese, Dutch, German and English, and english words are being added every day. JApanese newspapers have to publish thick tomes every year to explain all the new words they,ve used in the previous year, so they at least find coping with large volumes of new words a challenge.
My own experience is that, roughly, for every new player you attract because of exotic foreign terms, you lose one. For every player willing to take on the burden of new words you lose one who isn't. The upshot is that it doesn't really matter which approach you take to go terms - you end up with the same size population either way, just with different people.