One area where there is a clear divide is signage. The onyomi compounds feel more formal already, which is right for serious contexts like signage, and it also makes sense to use space conservatively on signs.
But like Vanilla said, we have the same thing in English. I think it’s a very common thing for beginners to express surprise at the existence of synonyms or very similar expressions. But the reality is that this is just the tip of the iceberg. There are probably 15 other ways to say this kind of thing that would be archaic or limited to very specific situations.
Languages tend toward a situation where all sorts of nuances can be expressed, not a pure economy of meaning, where every general thought can be expressed in only one way.
Is there a reason you think 電車の中 sounds strange there? It sounds better than 車内 to me in that context. I honestly don’t hear 車内 with regard to trains much except from signs and announcements.