Agreed. But on balance, exempting literally any combination is a trap. Software’s no good without hardware. And usually without other software.
You could ape the Apache 2.0 patent-scope compromise. But if you prefer to scope to the software as provided, I’d consider a more positive formulation, rather than swallowing permission granted with an exception. For example, from OSL-3.0:
Licensor grants You a worldwide, royalty-free, non-exclusive, sublicensable license, under patent claims owned or controlled by the Licensor that are embodied in the Original Work as furnished by the Licensor, for the duration of the patents, to make, use, sell, offer for sale, have made, and import the Original Work and Derivative Works.
The upshot is making the terms specific to complete applications, at least when wisely applied.