I didn't think that it did (but, once either docker or vms are enabled, those shares are created) If you run docker or vm's and prefer your own shares, nothing states anywhere that you have to use the default system ones.
If it really annoys you over the network, just set them to be not exported.
If you look at where unRaid was, where it is today, and where it is presumably going, some sort of system folder created automatically on the array is going to be required soon no matter what. Really not too much different than all of the folders Windows makes on your C drive.