A couple of basic questions regarding MSIX packages and their manifest files:
Appreciate the help.
An MSIX package can contain multiple applications, but applications in MSIX reffer to "shortcuts" if you want to think of them like this. Applications are the shortcuts that appear in start menu. Of course, you can capture multiple applications in your MSIX package (vlc, notepad, etc) and create one big MSIX package, but i don't recommend that.
Yes, everything that happens on the system is defined in the AppxManifest, but you can't specify what to install/deploy. If you capture 2 applications (vlc and notepad) you cannot chose during installation that you want only VLC installed. There are no such options. Of course you can leave all the files in the package, delete the Application entry in the manifest, and the user will only see VLC for example, but the MSIX will install the files for both Notepad++ and VLC on the machine, which again i don't recommend. Keep in mind that almost everything is stored in the AppxManifest file: startuptasks, FTAs, services, app alias, app extensions, firewall rules, etc.
Think of it like this, if you recapture VLC Media Player, it has 3 shortcuts. Each shortcut represents an Application: an application to VLC.exe, and two other applications to VLC.exe and additional arguments.