Having built a rather large app using SvelteKit, I found the routing scheme to make lots of sense actually. You always know what code is located where, concepts transfer everywhere consistently, and concerns are nicely separated.
This whole file-based routing wasn't a great idea to begin with, as a general solution to routing. It works (up to a point) for a static site generator, but most SSGs provide a permalink setting so there's an escape hatch.
The whole thing gets even worse when you start introducing issues like having dozens if not hundreds of files with the same filename, weird characters in folder and file names, etc.
It might look complicated at first sight, but once you actually use it you really appreciate the way it's structured.