He doesn't work for any organization/promotion. He's an athletic official for the state of california. That is the only state where he has recertified as a ref. The UFC hasn't run a show in Cali since he recertified. The athletic commission determines which refs will work the card. Obviously the UFC has some pull when it comes to those decisions, but the bottom line comes from the athletic commission.
Big John has said that he'll ref any event the state asks him to, regardless of promotion; cause that's his job. But as of now he hasn't gotten recertified in any state other than Cali (to my knowledge at least). And he said in a recent interview that he dones't have any plans to get relicensed in Nevada.
He is pretty tied up with his reffing/training academy BJMUTA
. I believe that's why he's focusing soley on california at this point.
If/when the UFC runs the next show in California we'll probably have an answer to this question. Big John has already said he'd accept a spot on the roster for a UFC card if he's requested by the state. So if they run a show there soon and he's not present it's probably cause the UFC pulled strings to keep him out.