Yeah in your case the best fix is probably REMOVING StartupWMClass from those launchers if it is present. Then it will only match the app id on the .desktop file name.
Honestly Gtk theming has extremely poor documentation and you need to look closely at existing themes to figure out all the CSS selectors you need to define. It is definitely possible, but can require some trial and error.
Not all themes are created equal, but the titlebar is actually one of the easier things to theme.
That being said, it really depends on your DE, and if the apps you are using are Qt or Gtk 3/4.
I really wish they had better guides online, but that was the main reason I spent time working on Celestial. To finally have the consistency i wanted, and untangle the theming mess.
StartupWMClass is NOT needed if the .desktop file is named correctly.