This post is a little dated but the install parameters are probably still valid. I notice there is a /NORUNONSTARTUP parameter which might be what you are looking for (Though you already found it in the registry) - https://forum.glasswire.com/t/support-for-silent-install/657/9
My issue was a little different than your settings resetting, but my computer wasn’t actually sleeping correctly when I closed the lid. I changed to sleep after 30 minutes and have not had my key deactivate in about a week and a half. I believe GlassWire was getting too many “License verification failed” events while I was not on the network, and was auto-deactivating my key.