Sorry Markus, I don't mean to pick on you. This is a great, healthy discussion and I just want to make sure that some assumptions die where they should, so thanks for contributing to the discussion.
CNC machinery (which I've spent my entire working career around) only make it possible to make the same exact mistake a shocking number of times. People like to assume that CNC means perfect when compared to an old man on a 100 year old conventional mill or lathe. Accuracy and repeatabilty are functions of machine rigidity (stiffness) and not the black box hanging on the side of the machine giving orders.
The case halves are cast (and rather poorly if you examine them), which are then machined in several operations before they are assembled into an engine. Each time you remove the casting from one machining operation a human puts the casting into the next machine. There is room for error and variation every time you touch the part, and depending on how the part is "registered" (that is, how they pick up previously machined features to index the next operation from) it can have a huge effect on the consistency of the finished product.
A loose chip in the fixture will cause variation, a cutter that is getting dull or has runout, how tight one operator clamps the part in the fixture compared to another guy, etc. I've seen marks in a part after a train went by the shop I worked in at the time and older machines could just take a left through the middle of a part on a hot day for no reason.
IMS runout doesn't surprise me since the thing is pressed together, and having a sprocket slip isn't uncommon.