Any instance is plausibly not xenophobia. Which ones are is hard to prove.
But in practice it is set up and carried out by people who often have some level of personal xenophobia. Thereby generating an institutional cover for personal feelings. The extent of this is impossible to verify. But certainly more than zero. And, anecdotally, likely far more than zero.
That the policies are not simply distributed in accordance with weak national financial controls is demonstrated by the fact that Patrick McKenzie (US citizen) has encountered these problems multiple times while trying to get Japanese banks to deal with US financial institutions. Japan does not doubt that the USA has strong national financial controls. But "foreigner wanting to deal with foreigners" still generates heightened scrutiny and sometimes real problems.