Why do you install Thunderbird from the AUR? It’s available on the official repository in Archlinux repos (and all distros based on). And updates are extremely quick. Can’t say anything about the Flatpak version, because I never used it other than “native” installation. I am using it since over a decade and don’t remember having crashes, maybe once in a while (1 time per year maybe fault of something else). I actually use Thunderbird with 5 accounts from different providers, plus use it as my RSS feed reader, because its stable for me.
I know saying “it works for me” won’t help you, but maybe its an indication that something else is wrong. I would recommend to install it from official repository instead.