What is the use case of a SD slot on motherboard?
It's for booting a hypervisor or lightweight operating system like VMware ESXi.
See: What happens when the USB key or SD card I've installed VMware ESXi on fails?
By installing an embedded hypervisor/OS on the SD card, you leave all the front-bay disks available for data storage. This is an useful logical and practical separation.
Some servers have two RAID1-ed SD slots: if a single SD fails, the system continue to run from the mirror, leaving you the time to replace the failed SD.
The most widely installed embedded hypervisor probably is ESXi, with a footprint less than 2 GB.