I'm thinking of stuff like the re-implementation of the IBM bios where the re-implementation had to effectively match a certain undocumented specification but not necessarily follow the actual implementation from the original bios

but in some sense clean-room reverse engineering does necessarily entail that certain things will be identical, and I guess the scenario in the article could be describing a situation where none of the final product matches the original template at all, so maybe it is slightly different, and in that case I guess there wouldn't be a copyright issue at all?

It would be more like how when movies are made they tend to use existing music as a placeholder until the final music is made, and it doesn't seem like anyone considers the final movie to require a license from the creator of the placeholder song even though the direction of the final work is often strongly influenced by its pacing