The system partitions in Chromium OS are somewhat special compared to those in traditional Linux systems. The System storage shown in FydeOS Settings does not only include the operating system itself. The system will allocate space for different partitions based on the total disk capacity available on your device. The space shown there represents the allocated space for those partitions, not necessarily the space that is actually used by files.
If you would like to investigate the actual disk usage in more detail, you can open the terminal and run:
df -h
This command will show the real disk usage of each partition.