It looks like it's in design, as you can see, by default, Windows Apps behave the same, even those that use a transparent color for their logo (for example, a calculator, mail, etc.).
However, if you set the background color of the logo and tile to βtransparentβ (in the application manifest), the icon of your application may appear in the Start menu with a transparent background in some cases, for example, when Windows is in a contrasting theme.
source share