I showed you one solution, based on PAR. perl2exe has similar caveats, and a similar solution (give pod2usage a text file with pod to read)

When running the EXE, it should work the same as running the script e.g.,.... Shouldn't this behave the same? Thanks

No. pod2usage reads $0 (a text file, a perl program) unless you tell it different. With perl2exe $0 is the binary file .exe, so you need to tell pod2usage to read a text file, not the .exe