[1] I use packager API and set VENDOR = myVendor
In the .wxs file I read:

Manufacturer="Unknown"

And in several places related to Registry there is a key value such as Key="SOFTWARE\Unknown\..."

In all these places the value of VENDOR might be used (this could be considered as a bug isn't it ?).

[2] Still in the .wxs file I read:

<Package Description="MyAppName" Comments="None"

The value "None" for Comments has little added value. It is readable in the HUD that comes up when you hover the MSI file (attached snapshot). I suggest to use the value of DESCRIPTION if it differs from the application name, otherwise to not set it (or set it to empty string if the field is required).

[3] In "Add / Remove Programs" the icon file isn't used. This is not homogeneous with what we get when producing an EXE with packager + InnoSetup (attached snapshots).
It seems simple to add the missing line to the .wxs so that user experience with MSI becomes as good as with the EXE: see http://wixtoolset.org/documentation/manual/v3/howtos/ui_and_localization/configure_arp_appearance.html
Today there's already these lines related to icon in the default .wxs file:
  <Icon Id="DesktopIcon.exe" SourceFile="MyApp.ico" />
  <Icon Id="StartMenuIcon.exe" SourceFile="MyApp.ico" />