Solid areas on the soldermask layer represent areas where soldermask will be removed. They represent apertures in the soldermask. If you make the array out of pads rather than solid regions or copper rectangles then you can simply apply a negative soldermask clearance to cause the soldermask to overlap the pads rather than have a positive clearance around them. So define a pad of the desired size with the required negative soldermask clearance first then copy and paste then use the Distribute Array tool to place them.

Perfect, thank you.