I have never used it to reccreate my current system so not sure on the files in home. My first thought is yes, anything to be put in /home should be under skel.
For choosing a kernel see the conf file.
manjaro-tools.conf is the central configuration file for all tools part of manjaro-tools. Only edit the general and the “buildiso” part to not exceed the scope of this tutorial. If you are not sure what and how to edit it, do not edit it. You can always use arguments with the buildiso command later.
By default, the systemwide config file is installed in
Best practice is to leave the systemwide file untouched and copy the system wide config to your home directory here:
If the userconfig is present, manjaro-tools/buildiso will load the userconfig values, however, if variables have been set in the systemwide config file, these values take precedence over the userconfig. Best practice is to leave the systemwide file untouched. By default it is commented and shows just initialization values done in code.