Linux Mint Customization /Cinnamon/

Irgum,

I don't run Cinamon myself, but I'll make a few suggestions.

I don't think you need ~everything~ inside .config.

There may be files in there that refer to your current user id.
Obviously, you would want to exclude those when you add data to /etc/skel.
(Use grep -r to find files containing your user id).

Visually inspect the files to see if they make sense to include.
A trick I've used in the past is to make a copy of .config in a safe place, and then delete files one by one from ~/.config to see if removing a file negatively impacts my system. If there is a negative impact, then that file goes on the list of files to keep.

Even after you've done that, there may be specific lines inside each file that may you may be able to remove. Some of the files inside .config store the last position and size of an application window. On a newly installed system, you probably want the windows on first launch to be positioned by the OS.

Also, inspect .cinnamon to see if there are specific lines that make sense to keep.

Lastly, boot into your customized iso in VirtualBox (or other virtualization application) to see if everything is working. If not, make changes in Cubic, create a new iso, and test again. You may want to use lz4 compression during testing. Even though the iso will be a little larger, it will be quick t generate.