I'd say the important ones are GetOpenFileName/GetSaveFileName, and the Common Item Dialog API introduced in Vista.
With GetOpenFileName, applications can perform customizations by providing a hook procedure, which would be impossible to translate to another API. If an application provides a hook, it must be given a win32 dialog that has a specific layout. https://docs.microsoft.com/en-us/windows/win32/api/commdlg/nc-commdlg-lpofnh...
The Common Item Dialog API also allows applications to perform customizations, but these are done through a COM interface which could be passed along to a native API that supported the same features: https://docs.microsoft.com/en-us/windows/win32/api/shobjidl_core/nn-shobjidl...
I'm guessing, though, that the dbus API does not provide for adding custom controls of any type to the dialog, so once again you would have to use a win32 dialog if the application requests customizations.
At best, you're going to be able to replace the dialog in some applications but not others. To provide the functionality in the general case, I think you will need a shell extension, but that would result in some confusing UI. I don't think there's a good solution to this problem.