Hi Jean-Christophe,
Your dealer might be right about the Targa bc they've been produced in lesser numbers than convertible, hence possible a better value on the 2nd hand market. Plus it's better looking and arguably more rigid, although I wouldn't track it.
PCM 2 entered production at the same time as the revised Boxster 986 which means shortly after the 996 mk2 was introduced.
Most 996 mk2 with PCM will have the PCM2 although the early ones still have the PCM 1 with audio tape.
For the pre purchase inspection, I'm not sure what it is. If you mean going to the dealership and looking at the car in detail, yes of course, everybody whould do that.
So for Germany, you can buy yourself a nice weekend!
Good luck with your research.