The controller puts a little bit of metadata onto the individual drives that says "part of RAID1 array". Then the OS loads a driver that reads that metadata and builds the arX device ... and it's the driver that does all the RAID functionality. IOW, it's a software RAID implementation. But, due to the metadata that is used, it's a software RAID implementation that is unique to that controller. Which means, if the controller dies, you need to replace it with the exact same controller. If you use gmirror, though, you can move the drives around to any controller and still access the data.
If the controller won't let you configure JBOD or non-RAID modes, then create multiple RAID0 arrays using 1 drive per array. Or, just don't create any RAID arrays at all. FreeBSD will still see the individual disks.