Sam,
Lots of really good ideas here. I want to divide my comments into two groups: appearance and functionality.
Appearance
As far as appearance, I would love to have some flexibility in the appearance in the OS X controls, but that unfortunately that does not exist. It takes a lot of work to get a different look with dialog controls because you have to completely go around what Apple provides as standard controls.
Someone wrote a library a while back that provides white controls for a black background, and Rhino uses that in a few dialogs, like what you see in Rhino with the Analyze > Curve > Curvature Graph On menu choice. However, the author abandoned that work a few years ago, so I cannot depend on that library working forever.
Apple has their own library of custom controls that they use for their “pro” apps, like Aperture and Final Cut Pro. But that library is not available to third party developers like McNeel. A little birdie told me that a custom controls library almost made it into Mavericks, but was pulled out at the last minute. I’m hoping that something like Apple’s “pro” controls will make it into the next version of OS X.
I like your recoloring of the the tool buttons. I personally find the current color scheme a bit garish, but that’s just me. The buttons could be recolored in Mac Rhino on the fly. There are over one thousand tool buttons, so it remains to be tested whether automatically recoloring then would make them difficult to distinguish from one another.
Minor quibble: in the coordinates view in the lower right portion of the viewport, it appears you have a CPlane button and World button. The CPlane one is the same color as the X, Y, and Z fields; and World is greyed out. Does that mean the World option is disabled? I’m guessing that you mean that CPlane is currently enabled and you would need to click the disabled World button to enable it, but clicking what appears to be a disabled control to activate it is counter-intuitive.
Functionality
I get your idea of modules, and I understand where it comes from. They are equivalent in Mac Rhino to the different tabs that are visible in each section in the right sidebar.
Allowing only two sections in the right sidebar is just a current limitation that needs to be fixed. Also, what “modules” that are available in each section should also be customizable. I personally prefer to reuse precious screen space by having the tabbed sections, but you could also have just one tab per section and lots of sections. That way you could scroll vertically through a long stack of sections to find the one you want, just like in Photoshop. 
One of my goals for Mac Rhino is to make it possible to get rid of as much clutter as possible. By clutter, I mean UI elements that do not need to be visible all the time, but easily called up when needed. Mac Rhino does not come set up with a minimal user interface, but intentionally starts with everything visible. That’s so a new user can see all the typical UI controls. But most of what is visible can be hidden until needed. Jeff Hammond has an excellent example elsewhere in this forum of what is possible.
So I would suggest some functional changes to your design. Currently in Mac Rhino there are some buttons in the toolbar that activate popover windows for Layers, Object Properties, and Osnaps. I think those are pretty important because they allow you to hide the sidebars, so I think those toolbar buttons should come back. You have the space in your toolbar, so it’s not a big change.
Mac Rhino also has a status line in the lower left corner of the window that gives important feedback to the user. That needs to be somewhere in your design.
I like the mini viewports in the sidebar, and have thought of something similar. My idea is to have a stack of three or more mini viewports on the right hand side of the main modeling view. They would be live viewports, in they would display drawing feedback while modeling in the main viewport. Clicking in a mini viewport would immediately make it the main viewport, and the current main viewport would take the place of the just activated mini viewport. Don’t know if the swapping viewports would be helpful or annoying - it needs some testing. The “normal” four viewports option would of course still be available.
Tabs. Yeah, tabs should be there.
Questions
You have a few UI elements that don’t have an explanation, and I’m curious about your intent.
The Command text field in the upper right corner has a disclosure triangle. What would that button do?
What does the gear button next to the Command text field do?
I assume your layout expects the user to use the floating command options dialog. Is that true?
In your mini windows, there is a button in the left side of the title bar, to the left of the X close button. What does it do?
Conclusions
Overall, very nice work. I’d like to get some of these things in Mac Rhino. We’ll see what Apple announces this June at the next developer’s conference.