USB is perfectly acceptable and very common - a pair of 16G or 32G quality USB sticks is fine and doesn't take up SATA ports which you may want for storage drives. I wouldn't boot from an M.2 drive simply because FreeNAS doesn't get any real benefit from a super fast boot device once it is up and running and they are still mighty expensive.
If you have plenty of bays and ports, you can use whatever small, cheap, low performance SATA drives you have on hand for the boot partition. This is a little more reliable than USB sticks but also uses more power which is why some people still choose USB to boot.
Cheers,
Matt