Sounds like it's a bit annoying, but you just deal with it because you have to. I guess it's a slight extra use of time, but nothing major?
Anyway, to get to the heart of it, you just deal with it. I don't even find it annoying, it is what it is. It's like being annoyed by the fact that elephants have long noses. It is truly, after all, what most of us here do for a living. Whether it's slapping a one-off regex on a log file to get the currency format right, or sucking down JSON from a REST API and presenting it in a nice mobile UI to tell you when your Uber will be here, we take data and munge it, then put a pretty face on it. So were I to have to deal with currency formats in a text file that don't match what the machine expects, I just transform it appropriately without thought to "annoyance" or "inconvenience", just that it needs to be done.
So do Europeans analogously refuse to use anything except decimal points, except where they have to?
Displaying English-formatted numbers is incorrect in the rest of Europe, and will confuse users. Programming languages handle this, but you still write pi = 3.14 in the code.
Note 123.456,78 is German, but Swiss is 123'456,78. I think.
(Displaying miles and yards, inches and 'letter' sized paper is also incorrect, but it's unfortunately not uncommon.)