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.
If I understand correctly, that is just randomness comes from parallel compiling and linking.
If 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.?
That sounds a lot like US9116712, but I don't think its ever been publicly said that Windows does this.