From the CBA:

The League will determine, in its discretion, a Player’s Salary Budget Charge according to the following formula, provided, however, that MLS retains discretion to lower a Player’s Salary Budget Charge in individual cases

Assuming I understand this (and other, similar passages) correctly, MLS can simply ignore a portion of a player's or players' salaries when calculating their cap hit. Sign Busquets for $4m yearly? MLS can say they're lowering the budget charge to max TAM.