I just had a look at a few filetype's configurations and it's really a mixed bag of styles.
Thats the problem with software development that is contributed by lots of different people :-D
I am not sure about the suggestion to document only in `filetypes.common`, in one way I see your point, its all in one place and the individual filetype files then work as intended, only containing settings that need to be overridden. But on the other hand it means that two files need to be open, the individual filetype to be edited and `filetypes.common` to read the comments and to find settings that the filetype file does not yet use, and since Geany doesn't do multi-pane very well nor multi-window, it will mean switching back and forward between them, not ideal.
The other way is to make all filetypes files a copy of `filetypes.common`, comments and all, with the unused settings already commented out. Then no commenting code is needed when the filetype file is copied, and users can add settings simply by uncommenting the one they want instead of having to copy it from `filetypes.common`. Of course that means maintaining them all when `filetypes.common` changes.