It might be more intuitive if this was the first travel app every developed. But I don't personally any other transit UI that uses this pattern, and that makes using the sncf search "the weird one" and not in a good way.
Google maps and Apple maps all work like SNCF. The first thing you enter is your destination and then you can optionally change the point of departure if it is not your current or default location.
I would say this is a pretty familiar and useful pattern in general: Necessary and mandatory info first, optional data which has sensible defaults later.
This is just your preference and not terrible UX. In fact I find this the more intuitive way.