The case halves are the same, and I believe the heads are the same also, however the induction and exhaust systems (particularly the headers) got greatly improved. DME programming was certainly part of the equation too.
Variocam Plus has something to do with it as well.
"Porsche's more recent VarioCam Plus combines variable valve timing with two-stage lift on the intake side. The two-stage valve-lift function is performed by electro-hydraulically operated switchable tappets. Each of these 12 tappets consists of concentric lifters which can be locked together by means of a pin. The inner lifter is actuated by a small cam lobe, while the outer ring element is moved by a pair of larger-profile lobes. The timing of each valve is seamlessly adjusted by means of an electro-hydraulically operated rotary vane adjuster at the head of each intake camshaft."
are the lesser cylinder wall thickness and the type of IMS fitted which is far more expensive to maintain/replace/upgrade. The 3.2 is said to be the more robust engine.