Regarding PTC Case C12509583, this needs to be fixed by PTC. They state this is intended functionality, but it causes confusion and can become an issue because an extra hole is placed in the pattern and the initial hole (cannot be removed from the pattern) is not in the same location as the point selected. This move is slight, but can be out of tolerance. A "work-around" is stated as the requirement, not a true work-around. This work-around is to go into the options and select Use alternate origin and then you can select a point in the pattern.
I propose that PTC does this automatically as they know that if the pattern is a point pattern, and the hole is a standard hole, then this fix must be applied. To me this seems like it would be an easy fix.