As the title states, if the main EXE is renamed and run on a server a prompt for .Net 3.5 is presented. The easy answer would be to not rename the main EXE from Deploy-Application.exe to ExampleName.exe. Thought it was odd enough to mention here.
The renaming is part of a standard that was started years ago and still works on workstations. We have recently been asked to start packaging for servers. Have agreed with the server team to not rename the main EXE. They will use Puppet to copy files locally, run the main EXE and then delete the files.