It is still common in the open source community for people to use the original meaning of hacker.

Actually the Open Source use of the term is already incapsulated in the extending portion of the definition I provided. Along with the modifying source code example.

Additional example : Kernel Hacking; Linux.
You're a 3rd party extending it beyond it's original design by modifying the source code to add additional or new functionality under the legal protection of the GPL, regardless if you do or don't make a PR that gets accepted.

The hackers you are referring to are security hackers or crackers.

Actually no. The definition provided is far broader as already shown.
The key in the definition is beyond it's original design , say for example I take source code from Grub and I extend it by adding additional functionality that allows me to play pacman directly inside it. This modification goes beyond the authors original design and doesn't just change a pre-existing feature from it's default setting like running a terminal command does.

Anyway, none of this is the point.
The point is that there's a hard distinction between a Hacker and your Average Terminal User running a command in a shell interface. Shell interfaces like that of ZSH, BASH, etc. only serves as a way for the user to interact with the pre-existing features of the system.