But they don't adhere to the system theme at all so every time I launch a flatpak it is white if it uses GTK; and they are annoying to launch via command line.
You can theme them with some overrides: https://itsfoss.com/flatpak-app-apply-theme/
I throw this in my .local/share/flatpak/overrides/global file in order to enable theming (the override directory may require flatseal? I forget):
[Context]
filesystems=~/.icons:ro;~/.themes:ro;xdg-config/Kvantum:ro;~/.config/gtk-3.0:ro
[Environment]
QT_STYLE_OVERRIDE=kvantum
GTK_THEME=<your theme name here>
Then you can put your stuff in your personal ~/.themes and ~/.icons directories
As for calling via command line, you can use something like this or just manually make aliases.