Welcome to the forum! 
Manjaro is probably the most stable of all rolling-release distributions. Even Arch Stable is already fairly stable, and serves as the daily driver for many people.
Manjaro’s Unstable branch is actually Arch Stable, and from there on, we test everything more thoroughly in the Manjaro Testing branch before it percolates into Manjaro Stable.
pacman does not offer any access to the AUR. pamac does, but that’s a different package manager, and as you say, AUR access is disabled by default. So people who want to enable the AUR will be doing so at their own risk.
That question denotes an XY problem. 
First of all, everything that you install from the official repositories is compatible, because it’ll have been tested by the Manjaro community, and by the Arch community before it even arrived in Manjaro Unstable.
Secondly, there is a reason as to why you sometimes need to update your system by way of the command line, as opposed to via a GUI — the GUI in question being either pamac-manager or octopi.
If you only want to install a few packages, or there is a small update with fast-tracked packages — these are packages that are regularly updated because of security considerations or urgent bug fixes — then it’s perfectly okay to use a graphical package manager. For bundled updates — I’ll get into this a little farther down — however, it is always safest to completely log out of your graphical environment, switch over to a tty, and run the update process from there.
Large updates are always bundled together in Manjaro, and this is true for both the Testing and Stable branches. Each bundled update comes with a dedicated thread under the Announcements category of the forum. The first post of that thread always details the changes that the update brings, and the second post lists the potential problems and how to work around them. It is imperative that people monitor said category and read these announcement threads.
As the matter of fact, there has been another Stable Updates thread today — just click on the link and see for yourself.
However, Manjaro is not necessarily a suitable distribution for everyone, and some people are better off not even using GNU/Linux in general. Not to toot my own horn, but I’ve written a short essay about this, which you can find below. 
Also, alongside the Wiki — and the excellent Arch Wiki — we also do have a very elaborate Tutorials section, in which you can find a great wealth of member-contributed resources. Take a look around in there as well.
Lastly, I will say this. With the disclaimer that I’m not exactly the average user — but then again, I also run a much more specialized and customized setup than most people here — I installed Manjaro on this computer over five years ago, and I’ve never had to reinstall. I’ve always faithfully and conscientiously kept my system updated and maintained, and Manjaro is my daily driver. I don’t use or have any other operating systems on my computer, and this is my production machine.