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.