Just had a quick look and it looks good.
I do have a few observations, numbered to make replies/discussion easier:
Panels Configuration dialog
1. Elements that must always be shown shouldn't have a check mark next to them as it implies they can be hidden.
2. Not sure why some elements have a text box that just reports on whether the check box is ticked or not.
3. The two elements available for the "Top panel" and "Bottom panel" don't warrant them having their own section. I know it looks more complete to match the rest of the dialog, but aesthetics shouldn't win over usability.
4. The "Overlay" checkbox is described as displaying "elements stacked on top of each other". You could just label the checkbox "Stacked?" to remove one level of abstraction.
5. There may be technical reasons, but some restrictions on where things can go seem arbitrary. For example, I can put the Spectrum visual at the bottom of the main panel, but not on top.
6. I think someone else mentioned it, but it would be good if movable elements could be identified without dragging them. For example, mobile UIs have little stripey "handles" to the left of list items that can be reordered. It also gives something "tangible" to click on to drag. Now I click things to drag them and think it's also going to change the checkbox state.
7. The sub-dialogs aren't implemented, so it remains to be seen, but the number of elements with a separate "Configure..." button are a little alarming. This is a great opportunity to completely rethink how some of these settings are implemented, not just move them around.
8. It's not a very scalable design for adding new elements in the future.
Main window
9. Little triangly pictures in the column browser headings mean "reverse the sort order" but in the element headings little triangly pictures mean "Click here to show something else". Different icons for the different actions would be better.
10. Only a minor thing, but it does pop up in a few places - the tooltip for the configuration button is "Configure Layout" but the title bar for the displayed dialog is "Panels Configuration". Consistency in little things like that help users remember which task goes with which button/control.
11. The context menu on the Thumbnail browser has a submenu, "Customise Panel", with three different thumbnail sizes. Unless there are more options to be added later (which is entirely feasible) these options should either be promoted to the top menu, or the submenu should be called "Thumbnail size" with options "Small", "Medium" and "Large". This also occurs in a few places, so thought I might as well mention it now while I've noticed it.
Bee excellent to each other...