You don’t seem to realize that this is equivalent to that. The user already made the choice to install a desktop environment which generates themes. So if you make the choice to build an application with GTK, and you want users to be able to use system themes with it, then consider it done.
To argue otherwise would make you a hypocrite. It would mean that you don’t actually want users to use themes, so you take issue with desktop environments which make it easy to do so by default. So if you want people to be able to use themes, then you shouldn’t complain when people choose to use a desktop which enables that use case.