The probability of a three of a kind at 4.98% is lower than that of a straight at 7.16%, due to the wild card rules. In Shuffle Master’s Fortune side bet, a Three of a Kind pays more. While they are allowed to have any rules they like for their own games (subject to the approval of regulators), I doubt Shuffle Master would have the audacity to change the rank ranking of the base game. Not only would the change be un-poker like, but it could result in untold complaints by disaffected players. I suspect the supervisor is confused with the three of a kind paying more on a side bet and incorrectly assumes that means it ranks higher in the base game.
This question was raised and discussed in the forum of my companion site Wizard of Vegas.