A comparison like
Boolean b = …;
if ( b == Boolean.TRUE )
does make sense. There are three valid states of a Boolean variable: null, Boolean.TRUE and Boolean.FALSE. All three are comparable via == operator.
Using equals() is complete nonsense for Booleans. Either you rely on auto unboxing and compare a Boolean with a boolean or you use the == operator to compare pointers like above.
Boolean boxes should be excluded from rule S4973.