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Tweaks are fine with a catch. Linux systems are fairly robust. I have found that when installing new software, the package installers are quite good most of the time in helping back you out, if you do not want what you installed. If something goes bad, you can usually find a workaround (delete a lock file or whatever). Usually, installing new packages does not bite you when you upgrade a system as opposed to performing a re-installation. I have found doing "special" things, like switching to the KDE desktop when Gnome was the original desktop installed cause problems when upgrading versions.
I am not sure why you would want to add a tweak to avoid the command line, because you can pretty much avoid the command line with Red Hat, Fedora, and Ubuntu, distros with which I am familiar.
As long as you are comfortable downloading and installing a tool like that what's the harm? I would at least try to snapshot some system files, and put them in a safe place; then try regular Ubuntu command line; and then try your tool.
I have used Ubuntu Tweak, and not experienced any issues. It is quite handy is you want to tweak things without going to thru various menus or terminal commands--it is a all in one tweak; e.g. nautilus right click menu to open as root in UT is as easy as checking a box.
that is my experience, others may have had it differently
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