How can I set up incremental backups to include my themes and customisation on Ubuntu 18.04?
The reason of the advices to not backup the "/" folder is this: typically, there are many virtual (and, sometimes, physical) filesystems attached to it. A virtual filesystem is like a /proc: it doesn't have physical files on the hard disk, instead listing/reading/writing their file structure manipulates some data structures of the kernel. For example, writing 1 into /sys/bus/pci/rescan doesn't write anything to anywhere on a hard disk, instead it re-scans the PCI bus for new devices.
Backing them up would be meaningless or they might be even harmful.
If your goal is to back up everything, then the best what you can do is that you back up everything. However, backing up / might be problematic because of the problem above.
However, there is a simple trick to solve that. Linux knows the thing so-named bind mount: it means, that you can mount a filesystem multiple times.
For example, a
mount /dev/sda7 /mnt/root
will mount your root filesystem (considering if your root is, for example, sda7) to the directory /mnt/root. You will see everything in it, except any sub-mounts, including the virtual filesystems.
The trick is this: after that, you can safely backup /mnt/root with any tool you wish to, including rsync.
Note also, this is only a recursive file copy. You have no protection for possible file inconsistency issues what happen. Imagine if a database has two files, for example, /var/lib/postgresql/11/main/base/13731 and /var/lib/postgresql/11/main/base/13732 which refer to eachother. If the database engine writes something into the first and to the second, while your backup process runs, then it is possible that the first will be backed up and the second won't. Thus, your database will become crap after a restoration.
This is also a reason, why you will probably find contra-arguments (sometimes quite vehement ones) against backing up your system on this way. However, in practical, user-level use cases, a real problem such this exists only very rarely, maybe the most typical one is when you are playing with a database for some web development task. In a home environment, I simply ignore this problem. In a professional environment, it is practical to use another, different backup for your data which is sensitive for this.
Clonezilla to the rescue. Atrocious console interface but gets the job done reliably.
Download image and make a bootable USB drive from https://clonezilla.org/
Boot Clonezilla from USB drive and back up your drive and/or partitions to USB drives or sticks for easy restore. Don't let the UX scare you, it really works.
If you really want to have a backup of just your themes and customization, then you don't really need to make a backup of your whole system. You just need to make a backup of some of your dotfiles.
For example, the changes you made for your windows are in ~/.config/gtk-3.0/settings.ini file. Most of the programs that you install will have a configuration file in ~/.config directory, you just need to make a backup of those configuration files.