You have accurately described the documented behavior of FileMaker Server with respect to folders. Any FileMaker files in the database (and alternative database) folders and one level down are opened when FMServer launches. Anything deeper is ignored.
You could create hard links to anywhere on the machine, but that's probably not what you want to do....
And, of course, no two files in any of the accessible folders can have the same name.
-- Drew Tenenholz