I've created a python script to make packing missions a bit more convenient. It zips everything into the pk4 for you, while auto-excluding unwanted files/folders that you list in a .pkignore file. You can also create the .pkignore using FM Packer, if you want. This script also allows checking for problems with files, and unused files and definitions.
https://github.com/Skaruts/tdm_fm_packer/releases
It's in an experimental state, so backup your mission before using it, and where possible double-check the results.