Hi. You ask a very good question. I’m actually almost embarrassed by the answer I’m going to give you, since I know from conversations I’ve had with others that what I do is not what is recommended, nor liked. But it works for me, so I’ll tell you, but remember, as Patrick Swayze once famously said, “opinions vary”.
What you have to keep in mind about my setup first is that I use a window manager, but I always install about a dozen DTE’s. Yes, I like to desktop hop to play so I load up nearly every DTE on my daily driver. I use a window manager predominately, but I can switch to any DTE to play with it, test it, use it to do tech support for friends, etc.
Why does this matter to your question? Well, and again, I’ll probably be yelled at by a lot of guys here (if only they knew who they were yelling at, lol), because what I do is, to say the least, unorthodox.
I use what you do, lxappearance, as my main gtk theming device. But like you, sometimes I find other apps do not follow my theme. So I change the settings in many and several theming controls, and this has worked out for me to greatly increase the consistence of the look and feel of my desktop. I’ll tell you what DTE settings I invoke.
I use, as I said, lxappearance. Also mate-appearance-properties, xfce4-appearance settings, and systemsettings5 (kde’s tool), I used to also use cinnamon-settings themes tool, but I’ve not been able to see any effect it has if I don’t use it. So that’s a bit of work, and I change my themes weekly (I’m into variety, so sue me!). But it’s only a few settings in each tool, and it works. Mostly. Much more than not doing this. But if you don’t want to install multiple DTE’s, I fear I have no good advice for you.
One final tip. If you use systemsettings5 from kde, make sure the application style widget style tab’s dropdown is on gtk2. Oh, and in cases where the theme tool doesn’t have the same themes, what I do is just find the closest match to the look/scheme I’m using, is all.
This is a kludge, I know. If anyone thinks they know a better way, that’s super, I’m always open to learn. But telling me not to do this will fall on deaf ears, because I do what I like, and I like doing this. I won’t change my way, but I’m happy to find a better road to get to it.