Thomas' opinion was a concurring opinion, not the majority opinion. He agreed with the finding of the court about the legality of appointing that guy to the NLRB but wanted to lay out a case against the constitutionality of the FVRA as it pertains to principal officers (only) under the Appointments Clause.
His argument is absolutely sound. It's one thing to use the FVRA to appoint someone to act as an "inferior officer" in an acting capacity, but it should not be used to fill a "principal officer" role under any circumstances because the Appointments Clause does not allow that.
So when Roberts said this in that opinion,
The President may override that default rule by directing either a person serving in a different PAS office or a senior employee within the relevant agency to become the acting officer instead, Roberts said,
he was wrong, or what? Isn’t this exactly what was done.