This is only an issue if the flag is the only information provided. In the case of the Swiss languages, you could use the Swiss flag for all for all of them, or only for the languages that are unique to Switzerland.
Words do not have to be unique in language. You can lead an army and you can lead water in a lead pipe.
> This is only an issue if the flag is the only information provided.
The next step is acknowledging that the flag doesn't contribute anything, but may cause confusion or negative associations with the flag's country. So what exactly is the point of using it at all?
One very useful property of flags is that the flag is the same in any language, even if the names for the languages are not.
Having a colorful icon is also helpful if you have problems reading text. Means you don't have to read all the languages' names that are on screen, you can do a coarse visual match by colors and then confirm by only reading the one name.
Modern low contrast monochrome flat UIs are a nightmare for people with reading disabilities and low-grade sight impairment. Speaking from my own experience. A dab of color does so much to help parse a UI. It doesn't have to be the perfect representation or unambiguous. Just give me something to help navigate the UI that isn't just monochrome text possibly with monochrome line-art icons.
Oh, yes, that's why I wrote that the language must be written in the native language and additionally contain the translated name. And _every_ long list of text should be searchable (for the native and the translated name).
The problem is that a list of languages has no alphabetical order because different languages use different scripts and there is no standard order of scripts (yes there is Unicode, no relying on your users knowing the order of scripts in Unicode is not good UI design). So there is no way to order a list of languages so that someone can binary search them like they would a dictionary.
Which comes first: Ελληνικά, العربية, Русский, or 日本語?
Flags assist by giving a second piece of information that can be used to identify the right language easier. They still perform this function even if the wrong flag is used. You can scan a list of flags with names faster than you can scan a list of weird unfamiliar language names.
Words do not have to be unique in language. You can lead an army and you can lead water in a lead pipe.