There is a `filetypes.perl` but no `filetypes.Perl.conf` because Perl is a __built-in filetype__, that is it is a base filetype, hard coded into Geany, and not dependent on any other filetype. Its not a custom filetype that depends on another built-in filetype.
For each hardcoded filetype, Geany has code that looks for a `filetypes.xxx` as the filetype is used by a file, but for custom filetypes it searches for all `filetypes.*.conf` files at startup and creates filetypes for each one it finds, so nothing needs to be coded in Geany. The custom filetypes files have a different form from the built-in ones so the built-in ones are not found again by that search since they are in the same directory.