Doesn't clean room typically apply to cases where the "dirty" team has legitimate access to copyrighted code, like the IBM PC BIOS which was published in the technical reference manual, and uses this access to write a functional specification for the "clean" team?

I'm not sure how clean room would apply to commercial applications distributed in binary form, as there's no way to look at even disassembled code without violating the license agreement and therefore being in breach of contract and subject to potential copyright infringement claims for copying or even continuing to use the software, let alone cloning it, and surely you're not going to be subject to a copyright claim based on familiarity with the application from merely using it.