In some sports, NT players are owned by the NT on "central contracts" who loan them out to clubs, but dictate when they play (and thus manage their fatigue).
Something like this could work for Buzzerbeater. At the end of the season, the NT coach could have the option of offering a limited number of players on the NT roster contracts with the NT association (with the owners receiving a standard compensation fee. Owners who turn down the offer would be committed to retaining their player for the following season). These players would be made available by the assocaition for B3 games only, and also play for the NT.
A B3 draft could be held to see who gets which players.
A number of variables would need defining (how game shape is calcluated, how many central contracts are allowed, what the compensation fee is, how the players would be allocated to clubs in B3, what happens to players who lose their central contract at the end of the season) but the essential idea might keep the highest salaried players available for NTs but take them out of league and tournament play where thye do more harm than good.