It will depend on what account you are using for SQL Server Agent service. 

If the %ProgramData% is a system variable it should be seen by any account on the server where the instance is running. Where, user variables are local to the user profile it was configured under.

**Edit**<br>
Good question on SF for [adding a system environment variable][1] has some good info on how you would add the %ProgramData% to the server.


  [1]: https://serverfault.com/questions/8855/how-do-you-add-a-windows-environment-variable-without-rebooting