If I look directly at the script, the call to sp_add_jobstep when using CREATE SCRIPT for this is:
@command=N'/FILE "<local-server-path-to.dtsx-file>" /CONNECTION "FlatFileConnection;"<unc-path-to.csv-file>" /CHECKPOINTING OFF /REPORTING E'
So it seems to me that the <unc-path-to.csv-file> somehow specifies the value of User::filePath or maybe the FlatFileConnection within the SSIS package.
The Job Step Properties for the SQL Agent job (in the UI) under General and then the Command line tab, have the Restore the original options selected, so where does the User::filePath get specified?