I've not tried rpi-update but I suspect that all would work if you mount the vfat partition in /boot.
I don't think there would be any problem with that at all. I hadn't bothered doing that on any pi/slack installs as it didn't seem necessary for any reason. perhaps that is how raspbian is set up since rpi-update was intended to update raspbian.
There is also the ability to use rpi-update to install the modules elsewhere. So if my vfat partition is mounted as /mnt/pi-boot I could do this
ROOT_PATH=/ BOOT_PATH=/mnt/pi-boot rpi-update
There's a few more options, if your interested look here: https://github.com/Hexxeh/rpi-update