I asked a Rosh Kollel that question. After checking he told me a Jew living in Israel cannot go to a place where there is an organized Jewish community (I assume based on SA OC 496:3). The fact that there are isolated Jews is not an issue (luckily since, unless you go to a real desert, there is always a risk of having isolated Jews). In my case, I was able to fly to an airport in chu"l on yom tov sheni since there was no organized community there.
The same ruling would apply to your question and allow a Jew living in Israel to go the isolated places you describe.
I have now seen that R David Sperling rules in the same way here
[...] there are major rabbinic opinions that allow it. This is because
when in transit you stay in the airport which is considered similar
to a "desert" (ed: despite the fact there are nearly certainly
individual Jews in the airport) – that is a place that does not yet
obligate you to refrain from labor on second day Yom Tov (see the work
Yom Tov Sheni BeHalacha, 3:11)
if you are already in a city that has a Jewish community in it
(and not just passing through the airport), it is forbidden to fly out
of it on second day, for it would be forbidden to drive to the airport
See also MB 496:10