Opening two images side by side within one instance of the app (with a splitter in the middle) might actually be a better way to have two images open at once though. That way, you wouldn't need 2 instances of all the panels/toolbar/menu, which would save you twice the screenspace. You would have one layer panel that would switch which image's layers its showing when you switch focus to each image. The selected brush and color would remain the same. This would be exactly how it works when you have more than one image open in photoshop.
It would also probably be more discoverable than opening multiple instances of the app, since not many apps support that and not many people are aware of the feature. And, probably easier to maintain in terms of development, since apple is probably going to keep tweaking how opening multiple instances of apps works behind the scenes. It would also avoid the question of what happens if you open the same image in both app instances and try to save one- which would invalidate the other. If they were both in the same app instance, it could gray out any image that is already open when you try to open a second one, disallowing it to be opened again and therefore avoiding the issue.
Art Studio Pro already can have multiple images loaded- this would be a real cool extension of that feature.