The reason is certain installers make additions or changes to the System file which are required for the requisite software to work correctly. For instance, if you just drop AppleShare Client 3.7.4 right into the Extensions folder and reboot, it'll bomb before it loads the control panels while booting.
Note that if any software has an Installer, use it - otherwise there is an increased risk of bombs and crashes. We start by going over the procedures to install the System software, then this page moves on to other topics of interest.
This supplemental addition to the Guide is here for more information about other vintage Mac activities and details that can be of use to almost any Mac user.