Custom buildscripts like those found in Arch User Repository is created with Arch distribution in mind.
Manjaro stable is usually several weeks behind Arch and therefore the buildscript may depend on one or more packages at a certain version. A prominent example was a recent glibc update.
Therefore the careful phrase is carrying a reminder that you should know what you are doing - know what impact the given custom package may have on your system, does it replace system files, what could potentially go wrong?
Themes is likely the most common cause of weird issues - e.g. when you apply a Plasma theme created for 5.22 and expect it to work on 5.26 or a GTK theme created for Gnome 3.24 - which most likely will not work well on Gnome 42.
So the careful phrase carries a warning that you may - depending on your system - cause problems by building and adding custom packages to your system.
Another example is toolkit upgrades which makes your custom theme behave weirdly, when upstream has changed the underlying theme engine - e.g. Gnome uses javascript as part of their theme engine.
A third example is Python2 which went out of service several years ago. Packages based on python 2 is moving to AUR and their dependencies is gradually disappearing - and suddenly you have a dysfunctional system.
Or GTK2 based packages which is also becoming extinct, and I could go on.
Think
- what impact does this or that script carry?
- do I really need this functionality?
- keep your system clean by regularly removing unused packages
dormant unused package may be the timed disaster waiting for the right moment to make you system unexpectedly to go haywire.