But the allegedly infringing content in the DMCA takedown in this case is (nonsensically) a trademark, so the safe harbor wouldn't protect SoftLayer against anything.
It's not functionally the same thing, because there is nothing here for them to be liable for.
"entirety of SoftLayer losing the protection"? What are you talking about?
How many times have we gone "how the hell did that decision happen?" with a patent or legal case? Seems like it happens daily.