It is my understanding that the SW Products provided are configured with generic rules so as not to miss anything related to the product in question.
Yes I know it would be nice if they only targeted core components of the product and not everything.
And yes, its annyoing that once you modify a provided SW Product, it will not be updated when a new catalog XML is released.
So, you can either modify the existing one so that they only target what you need, or create a new one yourself so as to preserver the original items allowing them to be updated.
I believe a software license only allows you to associate a sw product and not an EXE, so you have no choice if you wish to use that license attribute type.