You bring up several good points.
As you undoubtedly know from your industrial experience, it is almost never a good idea to have a control program shut-down with only one click. Hence one reason for a two step process. The way its done in Quicktrol is one way to do that and has nothing to do with the contest.
The first screen, Configuration, as noted in the information, contains the text labels for the gauges, switches, sliders and status lights. They are optional and do not affect the running of the program so are not explained rigorously during the first installation. Also noted in the docs is the purpose of the check boxes for the switches.
The second screen, with only reference to Com ports, is for setting comm parameters, again as described in the docs. Oddly, no one has asked that question before.