I don't think mklive will do everything you want here, but it can be part of the solution as you can use it to keep an up-to-date install medium. You'd need another method for backing up configuration and user data.
This way, your restoration strategy would consist of installing the OS from your most recent install medium, then restoring your backed-up configs and user data. This is the method used by some commercial backup/restoration solutions I've worked with in the past.
You'll need to specify the packages beyond base that you want, but if it's just all of your presently-installed packages, you could just use xbps-query to generate a list of all manual packages on your system. Something like this:
-p "$(xbps-query -ms '*')"
This will print the package and version numbers. I don't know if this is a problem, but if it is, then you'll want to edit those out. something like this should do the trick.
-p "$(xbps-query -ms '*' | sed 's/-[0-9].*//')"