Er, I think you have misread jms222's comment. He's suggesting that a lot of GNU'd code was inspired by BSD'd code which, as BSD is more permissive, is probably fine.
Which begs the question as to whether or not such GPL code is appropriately licensed. Some guy lightly alters some BSD code and then whacks GPL all over it. That's a bit disingenuous, even if permitted by BSD. For the avoidance of future doubt such code should at least come with some statement of origin.
In this particular case, if the relevant sections of VMWare's code also has strong similarity to chunks of BSD code then I don't really see how Hellwig will be able to sustain his case. The SCF analysis compared the entire Linux code base with the entire FreeBSD code base; what would also be interesting is if they repeated the analysis of the lines Hellwig wrote for Linux with the equivalent in FreeBSD, a much smaller and more focused comparison.
On the topic of the SCF's comparison of various functions, the fact that there is no consistency to the ratios of similarities suggests to me a lack of whole sale copying. A straightforward copy and obfuscation would surely result in more evenness between the various functions they've analysed. Whereas in fact some are barely similar at all. Also, after all that work, where's the side by side comparison for us all to see?!