Sorry for the late reply ( my network connection is dead and I am on a borrowed machine at the moment), the mounting holes are just holes, they don’t (or shouldn’t) have a connector id. Thus Fritzing doesn’t change them to red as they aren’t a connection but if you set a non zero copper ring they should be plated through (which it sounds like they are) although you don’t necessarily want plating through on mounting holes (to eliminate it set the ring width to 0). As to your pads, I just got back the boards I made with the new pads here:
and they appear to work fine. You may want to switch to them. They are smaller than the ones in the original shield but allow stacking connectors and will route a standard width trace between pins without drc complaints.