If anyone would like to buy me one of those fancy high res laptops, I'd be more than happy to take a deeper look at this. :-)
Seriously, I grabbed a utility last night to allow me to run my MacBookPro at full retina resolution (2880x1800). Setup my Parallels VM to run full screen at that resolution and set it to large fonts and could definitely see a bunch of issues. I fixed most of what I saw. Hopefully 4.0.16 will work better for you. If you see other major areas of Text boxes being cut off (mostly not tall enough), let me know where.
The next thing I think we need to consider is the toolbar size for the non-effect toolbars. They seemed very small at that high of a resolution. Sean may need to create some larger icons for those bars as well.