When you open a file, it copies it, renaming it in the process.
You can manage the files yourself and point it at that, but the default, eg. if you choose to open a file from any old place, is to copy into its own naming and organization scheme.
That is not the default when you install iTunes it asks you whether you want it to “manage your music”. This is not a new behavior - note the date on the above post.
Literally iTunes does this, by default, without changing its configuration.