I placed another (custom PNG logo with height 512px and weight 512px) next to the original logo.
That is located in the Atlas_Core.Content (So module Atlas Core and then image collection named Content)
Then in the navigation profile select your custom PNG as the general Application Icon and it did show up correctly.
Also within version 9.0.5.
So is your PNG file exact that size? (512 x 512)
Found it! Thanks for the help!