"so I think Inline::Files is acting really weird, instead of writiing to an external file, it writes to a new data section in my script."

Far from being "really weird", that's actually documented behaviour. It even alerts you to this behaviour in the WARNING section which has two paragraphs:

1. "It is possible that this module may overwrite the source code ..."
2. "This module is still experimental. ..."

I have used Inline::Files for demonstration purposes only (particularly on this site) to save having to create and list multiple input files as well as the source code of my script. I have never used this module in production and, given its experimental status, never intend to.

If you are using this module in production code, I'd strongly recommend finding an alternative, non-experimental solution.