Well, it was designed like this. all loaders used that format, because of the first released method using it.
to prevent having too many possibilities and user's side errors, it was decided to limit the working layout to a short convention list.
all filename need to be titleID6, subfolder need titleID6 but can contain the game's title for easy management by humans (we allowed 2 different subfolder's format to put the game's title in it, before or after the ID6).
No other USBLoader work with different format. Making one loader accept a different layout would break the compatibility with others, users wouldn't be able to swap the loader any time they want, they would need to rename all their library to the most common layout, so it's best to do it from the start.
filename.ext could be a problem if the filename is only 6 letters, the loader would consider it a GameID and will not find the game's cover and information in Gametdb.com database.
The only format working with other loaders but not yet in USBLoaderGX is this one, for gamecube games only :
/games/filename.ext
it's the default layout for devolution.
compatibility was added at a later date to
nintendont, and USBGX has not been updated yet to support this layout. the other layout work with all other loaders : DM,DML,Quad,neek2o,Devolution,
nintendont.
I know I could add it, but it would break "hot swap" of loading method, the games would not be in the correct path/format for all loaders.
you see why conventions are useful from the start. but I'm not against adding it later, just miss time to complete the gamecube's code part.