If nothing appears in /sources.list.d/ then you are ppa free
I do not know the mechanics of the software boutique and one of the first things I do is update it. You say they appear, but I would think that they could not install when clicked on. @lah7 is the brains behind this
As far as I know Software Boutique keeps its own list which references the PPAs, but they are only added to apt as needed (i.e. if you actually decide to install software or updates from the SB that come from a PPA).
Many software are from the Ubuntu repository in general.
Skype
Google Chrome
Uses Google's official repository.
LibreOffice
This is pre-installed, and uses Ubuntu's repository. There is an optional "Upgrade" button which adds LibreOffice's official PPA containing new versions of software.
Rest assured, all external sources are trusted and have been tested to ensure it works before the application is added to the Boutique.
As @anon42388993 points out, it's important to keep Welcome up-to-date (which adds its own repository) so that any source changes are immediately updated.
To answer your questions:
You can manage third party repositories from Software & Updates (under System → Administration). If you remove software from the Boutique, it will remove its PPA/source too, if applicable.
Boutique does include third party sources, and these are explicitly stated for each application. Boutique adds its source before installing (if applicable). It's the equivalent of somebody adding them using the terminal.
What is very important if you want "non-free" software is that you activate the "Canonical Partners" repo's in Software & Updates > Other Software otherwise you cannot install Skype from the Ubuntu repo!.
Thank you everyone for such detailed answers! I am very glad to learn that Software Boutique does not add PPA’s unless if I install something that requires one!