Why can’t i get grub-customizer from flatpak
Because it was not published to Flathub.
Check if your distributions packages provides it.
Also: Editing the GRUB configuration can, if done careless, break the system boot process, making for a difficult repair process.
So, even if using a tool to ease the editing of the configuration, you should really understand the changes being done before changing anything there.
The actual problem is that not all distros care about your Grub configuration changes. They usually avoid some settings.