Your question starts off sounding like you're the sort of person who has made your question to be a problem, but reading through it with an open mind, it seems like you're one of the people who is just confused by the situation and don't understand about the other people who make it never OK to ask someone with whom you are conversing online if they understand English.
The problem you're encountering is that there are more aspects of communication than understanding the language. Different people have different mindsets, and look at the world in different ways. Not understanding what someone really means when they've written perfectly good English does not necessarily mean the person who didn't understand doesn't know English. To an extent, you get this, because otherwise, you wouldn't even consider asking the question.
But most people when they ask the question have already predetermined the answer. They're convinced the person who they're talking to doesn't understand English at all. They are, at best, putting the words through a translation program, and pretending to understand English.
These people haven't really kept up with translation programs, because these days, Google translate is pretty amazing. I've had several conversations with people using Google translate on my end, while they write in their native language and also manually translate. Since 2017, Google translate seemed to convey their intent far better than their translations 100% of the time.
But that does nothing to help people who are looking at problems the wrong way to understand them better. I'm autistic, so I know a lot about difficulty communicating with people due to not being able to communicate the mindset properly. That's my always. But knowing different things are different, I try different approaches, and find some work better than others.
Also, while it's true that there are times when people who are not native English speakers talk, they say things in strange ways, it's also true that there are people whose native language is English who say things in strange ways. I should know, I'm one of them. You should know, because you're clearly one of them, too.
To address the question that you were talking about asking in the last half of your second paragraph... Anyone who would think it was rude for a stranger to ask them if they thought they were fat would think that it was rude for a stranger to ask them if they would think it was rude for a stranger to ask them if they thought they were fat. Moreover, most people would recognize that and feel there was an issue at the other end of that question even if they wouldn't be offended by the question being discussed.
To enable you to experience what being on the other end of that question is like, would you think it would be rude if I asked you if you've ever been tested for autism? Please understand that I'm not actually asking that question; this is an answer, and I am not able to ask questions in an answer.