The term "clean room" has a well established meaning you probably aren't aware of, I refer you to [1], it might clear up what the original reply was referring to.
So what? That's not a valid excuse to distribute modified binaries to the public. If the "first" team wants to look at binaries to do their documentation, they can download the official Skype client from skype.com. Why do they need to download a hacked binary from Github?
I understand the rationale behind it, I think it is wrong and has bad implications for the future.
No it doesn't.
The Wikipeda link[1] mentions the original IBM PC clean room implementation by Columbia Data Products.
It doesn't have the complete story of that, but from memory the way it worked was CDP had one team documenting how the BIOS responded to inputs, and then a totally independent team reimplementing that behaviour.
Most clean room implementation don't have access to a specification, let alone source code.
From the ruling: "Some works are closer to the core of intended copyright protection than others. Sony's BIOS lay at a distance from the core because it contains unprotected aspects that cannot be examined without copying. The court of appeal therefore accorded it a lower degree of protection than more traditional literary works."
Thus one could try to make the same case for Skype.