IMO GUI software centres can be very helpful for searching for software the user is unaware of. Discover is probably the most visually appealing and informative of the GUI software installers. I keep pamac, octopi, and discover installed, because each is better at some things than the others. Truthfully I rarely use them nowadays, but I still keep them installed because they are handy to have when looking for a specific type of software. However, I have not used them for updating for many years as they are nowhere near as reliable as the terminal for updating.
I think it might be a reasonable idea to have a pop up warning against using pamac (etc) for updating after first installing Garuda. Something similar to the warning that pops up when the system is overdue to be updated wouldn't be too intrusive. As long as the warning could be dismissed permanently, I don't see why people would object to that. That way the user had fair warning, and if they muck up their system by using a GUI updater, then they have no one to blame but themselves.
My take is this. I'm experienced with Arch so no stranger to CLI. Just make recommendations that every new user will see. Make your recommendation and explain why clearly to even new users.
Pacman is my preference for package management in all FOSS. I love that with the chaotic AUR I don't need an AUR helper in addition to pacman. That is a great value for Garuda. I want to see and respond to all package management messages. Include that capability and that it is best practice in your recommendation. It also helps us to learn about our software.
I sought out and use the chaotic AUR package list to look for software when pacman -Ss gives me options that I need investigate or when I want to look into the level of activity for a package. I did this with the AUR itself and I still use the Arch package list this way. So far I haven't had to have anything not provided by the repos including the chaotic AUR. If I do I'll look up the flatpak options and get it via CLI.
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