"Select the program that PRTG executes. You can choose from *.exe, *.bat, *.cmd, *.com or *.ps1 files located in Notifications/exe subfolder of your PRTG installation."
Why is there such a limitation? What about powershell commandlets? Those aren't stored in your exe folder. Why would they, right? They're stored in powershell's own folders and don't need to be referenced by path as powershell loads them immediatelly during its load.
But please answer also the general question, why don't you allow PRTG to start executables outside of its EXE folder in general?