Yes, but there is less stuff you can assume to already exist on a Linux desktop environment than on a Windows one, so you either need to bundle those with your application or have them as requirements.

Sure, see for example: https://www.flatpak.org/

I am waiting for the next big thing, where the 3rdparty programs comes as a virtual machine image with a complete OS in it, with own kernel for maximal platform-independency.

Isn’t this kind what java is already? And also if there is another OS running in this VM, this would lead to less efficient executables as you’d have to partition resources like mem