PayJoins help bitcoin users preserve their privacy because they bring ambiguity into blockchain analysis. Today's PayJoins are blockchain entries that are many-input and 2-output transactions. So the fact that multiple users can contribute inputs to one transaction breaks [the oldest assumption in blockchain analysis]. Still, lesser known "unecessary input heuristics" identify potential PayJoins:
Today's PayJoin clients avoid creating transactions that conform to UIH 1. This heuristic assumption is usually right. The heuristic assumes wrong if the change output is of much higher value than the payment, which is unusual. BTCPayServer code will not create these types of transactions.