I think the licence text itself is fairly straightforward (as much as legal agreements can be "straightforward") about it:

     each Contributor hereby grants to You a [forever lasting] 
     patent license to [do anything with] the Work

The key part being "the Work", which is the code (in source or binary form) that's covered by the Apache licence. A derivative work would be covered by this patent licence, but a clean-room re-implementation of a feature would not because you are no longer dealing with "the Work".