Parts and Serviceability
Is the 2.7t engine easier to work on than the M96 engine? Maybe... Since the 2.7t engine will not have much access to the valvetrain once in the vehicle, this could be inconvenient. There are a few items that should be replaced "while the engine is out" and this will avoid dropping the engine to make repairs. Chain tensioners, PCV spider assembly, and fuel injectors are not accessible whilst installed in the 996. As long as these items are replaced with new parts before installation, you don't have anything to worry about for 100k miles.
There are many things that are easier to work on the 2.7t engine when mounted in the 996 vs. the Audi that it came in, such as: turbo, wastegate, AC compressor, alternator, starter, etc. The timing belt and water pump CAN be replaced in the 996 without dropping the motor. You would only need to remove the engine support bracket and support the engine during the procedure. Ignition coils and spark plugs can be accessed without removing the engine, it's just a little tight.
Another obvious reason to favor the Audi 2.7t engine is cost of maintenance and repairs. Practically ANY part you will need for your Audi engine will be cheaper than the Porsche equivalent, will be easier to find, and will have more options for aftermarket, performance, OEM or OEM equivalent parts.
There are a fair amount of mechanical similarities between the Audi and Porsche engines too. The power steering pumps are interchangeable and the bellhousing bolt patterns are close enough to not need a re-engineered adapter plate, and the clutch and flywheel outside diameters are the same size. With all of these facts taken into consideration, the goal was to create something that could've rolled off the line in Stuttgart.