In Patrick Rothfuss's book Name of the Wind, he describes a fictional library called the Archives.
Every few decades, the master archivist dies, and a new one takes over. This new archivest has a much better plan for re-organizing the library than their predecessor. They immediately set about re-organizing the library.
But, this takes time. There are millions of books ("Ten times ten thousand books."), and it's more than any one person can re-arrange in their lifetime. So they start to, and then, invetibably, they die, and the next archivest takes over.
But it's worse than that! Some of the sub-librarians don't agree with the master archivest, and so they feud and quarrel and hide books where they think they should go. They continue sorting them under the old system, or the system before that. And soon no one knows where any of the books are, because everyone has their own ideal system.
Any system would be better than a hodgepodge of systems.
If you are working on a project, or building a new codebase, follow the conventions of the local files. If they are truly abhorent, affect change, but do it with consent, and in small strokes, cleaning up as you go.