[1PorscheBoxster986]

These M96 engines were Porsche first water-cooled engines. There were revisions made to address common and/or future issues during the production cycle. I think the % of engines that were affected were so small so this information is hard to gather.

As Paul mentioned, Porsche will sent out a refurbished engine to the dealership and the techs just install it. The dealership might not have the information on the refurbished engine and what was done to it before. The engine was covered under warranty as you stated so the car wasn't abused or tracked enough if any for Porsche to deny the warranty under abuse.

The cracked cylinder heads affected some S and 996 engines which resulted in the coolant/engine oil intermix as rfuerst911sc stated. This is more likely than the engine porosity for your year.

Whatever Porsche did to the engine must have been the latest shop revision at that time to fix it and pass a thorough inspection.