Haven't Clasen and several other devs on the issue tracker you and I linked above clearly has statements like "linking to libadwaita is an explicit decision to use the Adwaita theme" and "core GNOME applications linking to libadwaita will then thereby require that every distribution shipping GNOME is forced to consent to having Adwaita as the theme".
The only way a user's own custom theme will be used if a proposed opt-in flag is added to libadwaita (doesn't seem like it will be, recoloring API is being favored) and app developers use that flag.
Correct me if I'm wrong in this point and I'd be happy to go back and talk to the GTkeddit developer again but from what he independently tested, he seems to have reached the same result as I think.