Fuse is already installed as part of FreeNAS. It is typically only loaded when an NTFS formatted drive is mounted. To manually load it, you've two options. One is psuedo permanent, the other is as-needed. The first option is creating a system tunable named fuse_load. This will load the module at every system boot automatically. The second, is opening a shell and running 'kldload fuse'. You can unload it with the opposite, 'kldunload fuse'. You can check which kernel modules are currently loaded and what settings each have using 'kldstat'.
Mounting drives in root is definitely NOT recommended, however it does work (I've done it periodically for quite a while). Just make sure to explicitly call out every log location and everything else you are using or they will start writing to memory only which will both eat up your resources pretty quickly and possibly crash your machine. You'll also lose everything with reboot as it is entirely volatile that way. Once it is mounted at root, you can pass it to a jail or VM as usual for any local drive.
Mounting in jails is NOT currently supported. Although BSD has Fuse listed as jail-friendly since 11.2 iirc, for whatever reason it is not in FreeNAS. I've not dug into it deep enough to see if I can flag it friendly myself anywhere.