Most likely not. Its been quite a problematic way to update over the years (and that is putting it lightly). Not to mention the garuda-update does much more than just updates, it also does fixes if needed. You can also set it to update AUR packages as well. Take a look at Garuda Update | Garuda Linux wiki for more information.
If you find you still need a GUI package manager, I would check out Bauh. I usually use it to manage my Flatpaks, but it is still fully featured apart from that. Also, I would update with garuda-update before using any GUI package manager.
Proton-GE-Custom is also from the Chaotic-AUR. The version is slightly behind because Chaotic-AUR pre-builds the packages for you and thus it takes time for that repo to catch up.
I ran into something similar. When you open a terminal and update AUR via 'Yay -Syu' (the method the Arch wiki recommends to update AUR) it said I had updates, which none of the other methods had, including Garuda-update, or Bauh. So then I looked closer at the exact packages it wanted me to update and notice it was trying switch a few packages that were either from the Arch repos or Garuda-Aur repos to those in AUR. Not sure why it chose those few (I think 5) packages to switch, but I stopped updating AUR this way.
I just use Bauh which seems to work for all; Arch/Aur/Flatpack, etc. , and if there are major system updates, I will then use Garuda-update instead. It is all very strange.
Edit to add: I do know why it wanted me to switch those packages, because those 5 packages were more updated in AUR than they were in Arch/Garuda-Aur. To me, that is kind of dangerous switching packages to AUR.
Probably not unless you really need something that's not back in Chaotic-AUR yet. If you do, it should probably be after running garuda-update so any fixes can be applied, and you get a fresh mirrorlist. If you don't see something from garuda-update it's almost definitely got some reason behind it.
We are trying to get a lot of missing packages built still. Feel free to post new issues here for anything that doesn't exist at the moment. Do check for existing ones that we're currently tracking
I didn't know you could add updating AUR via Garuda-Update, thanks. Question though, will I run into the same issue that if a package in AUR is more up to day, it will try and replace it with the same package I have installed from Arch/Chaotic-AUR?
I haven't ran into that issue so I'm not completely sure, but given the wording "Update AUR packages via paru/yay after system update." I assume it does it for packages that were installed via the AUR exclusively.