PTE describes positions and sizes of objects using percents. Pixel values are not involved. So, if you work in O&A using percent (%) for the inputs of Pan and Zoom, the precise values of "Virtual size of slide" don't play any role, provided that the entries describe the correct aspect ratio. So, for any 16to9-project it does not make a difference, if the virtual size is 3840x2160, or 1920x1080, or just 16x9.
The situation is different if you work with Pan and Zoom in the uncomfortable way using pixels (px). In this case you should chose for virtual size the resolution of the device on which in the end the show will be presented. Nevertheless, as said above, in PTE's project files pixel values for Pan and Zoom will not occur. Everything will be transformed to percents. And working in O&A with percents allows you to position the objects with high precision.