Sorry, it can't be done.
1) Create 2 different patterns each with different skip points (you can even link the offsets and instance numbers together using global variables/equations), then suppress/unsuppress the patterns for each configuration.
2) Don't skip any, but instead use delete face/patch fill and suppress/unsuppress that as needed in your configurations.
I don't believe you can do it directly in the pattern, but you can go ahead and create the pattern, then right-click on the component you want to skip and choose "Configure Component", which will open a simplified design table that will allow you to suppress it for selected configurations.
When this was required I had multiple patterns in the first instance with each one controlling the desired end result. In the individual configs I suppressed or unsuppressed to have the desired outcome.