My issue with this analysis is that it suggests that large fortune 1000 companies have only one web server, have made only one technology choice, and it is up for display at the front door. This is a fundamental flaw in their theory that their results are more significant than the Netcraft results. All they are showing is what these companies use at the front door. These sites don't typically do much aside from showing flashy pictures to visitors. Large companies have 10's if not 100's of other internal and external web sites for dealing with a variety of constituents. What are those other sites running?
Of course, it's very difficult or impossible to find out, but I'll bet there is a mix of technology across all large companies such that you can't make the blanket statement that Company X has chosen Apache or IIS. Life just isn't that simple.