My take on this, as a Windows user, is that applications which are not part of the operating system ought to default to their own icon. I don't know if this is the Linux sensibility, but at least one advantage of doing this would be that Geany defaults to the same thing on both Windows and Linux. Personally, I think third-party apps should have their own brand, whose default is chosen by their creators. If their creators would like to blend in with the OS by default, then that should be their choice. If they would like it to be the user's responsibility to make the app blend in, then that should be fine as well.
So my vote is, use Geany's own icon by default. Linux users who like everything to blend in should know the ways to make it happen for themselves.
John