Apparently the only way to make a skin work with VE is to edit VE itself. This makes it very hard to make new skins compatible with VE, despite more and more third-party projects desiring such compatibility.
It should be the other way around - compatibility should be in the skin, not VE. The skin should be edited to meet VE's expectations (maybe have appropriate ids or whatever on things where it should be showing up around the content, or a js snippet specifying how it is supposed to show up, or whatever?), and modified and styled appropriately to look right with it.
And how to do this should be documented somewhere so we can actually, well, do it.