They're not encoded, but the code blocks are shuffled. That's why disassembly does look straightforward, but it used to thwart BinDiff at the time.
replyIf I understand correctly, that is just randomness comes from parallel compiling and linking.
replyIf you saying there is a whole step just scrambling blobs, i will be very surprised.
What made you believe this is the case? any examples/links/etc.?
replyIt was a part of our Windows build process when I was at Microsoft. I only assumed that they would keep doing it, but they might have as well dropped the practice.
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