This is just The Register’s style. Sometimes I appreciate the snark, but other times (like this) it’s laid on so thick it’s hard to understand what is actually being reported on.
I interpreted it to portray security personnel checking people's bags for contraband at an airport; where Microsoft is the security guard, and individual computers are the bags.
What an odd article, also the whole paragraph about the update having been scanned for malware and is stored on secure computers, isn't that just boilerplate for all downloads?
The Register is a British tech site that's known for its sarcastic, often informal manner of writing. They're probably including all that specifically because it's so weird that Microsoft even said that.
It would be a bit like a man with a Russian accent offering you tea and finishing with, "and there's no polonium in it."