In the solidworks API there are a couple pieces of examples for creating a hole wizard feature using the solidworks API. My issue with them is that it creates 1 hole wizard feature for each hole, even if the holes are identical. Additionally these holes use a copy of the hole location data and do not reference the sketch used to make them. In the Remarks for HoleWizard5 it mentions "To add a hole or slot at one or more locations, call IModelDocExtension::SelectByRay with Mark = 0 for each location." I have not heard of rays before, but it seems like it could be a solution to the problem.

Functionally I'm trying to do something similar to the following, just with API calls instead of manually. When doing it creates holes that are orthogonal to the sketch plane with predefined settings:
 

What the example does is the following, the sketches are not referencing the sketch, the holes are being made orthogonal to the direction it is being viewed at and the holes are split up into multiple cluttered features: