WB skins [components of] the Explorer shell. Dopus can be set to 'replace' parts of that Explorer shell.
No, Opus is NOT a shell replacement like Litestep.
Opus only 'replaces' Windows Explorer, the file manager, not the shell.
And all 'replaces' means in this context is that it takes over the filetype association for folders so that when a folder is double-clicked (or whatever) the folder opens in Opus instead of Explorer.
With Opus installed and in Explorer Replacement mode, Explorer.exe and the Windows shell, desktop, taskbar, etc. are all completely unchanged. You can still run Explorer manually/explicitly.
I'm sorry but saying that Windowblinds has to target dopus.exe and break parts of its UI (it is not just the File Open dialog), while failing to skin other parts, just because Opus can take over the folder association is nonsense.
Also, everything looks fine -- and is fully skinned -- if you copy dopus.exe to test.exe and run that instead. What Windowblinds is doing to Opus is not necessary and is causing problems, not solving them.
DOpus has its own 'skins' and they don't play well with WB. Never have...
There were some compatibility issues in the long-distant past but as far as I can tell they are all gone. They were mainly due to Opus adding icons to the titlebar (which it no longer does as it conflicted with Vista/Aero, and people kept clicking them by mistake so we just got rid of them). But if the titlebar was the reason for this strange 'compatibility mode' that WB uses for WB.exe then that is strange because WB still skins the titlebars; it's just everything else that is either inexplicable unskinned (buttons, tab controls, etc.) or outright botched (the top of the File Open dialogs, and for one user the top of normal windows whenever they are maximized; both having to do with the region of glass at the top of the window frame, so I suspect both the same underlying error within WB).
There were also some issues with the Preferences dialog in Opus and certain themes, but I think they were all* fixed a long time ago as well, and Opus itself used to detect Windowblinds and do things differently then (it no longer does as it should not need to) so even then WB should not have needed to detect Opus. (*Exception: One fairly obscure issue with the Prefs dialog was fixed very recently, where if a theme drew the tab control background without using a bitmap then the Prefs dialog looked wrong. Not many themes did that but it's fixed now, in the latest beta version.)
These days, at least from a quick test with dopus.exe copied to test.exe, Opus picks up the WB skin just fine so long as WB isn't targeting it for some weird mode where it messes up titlebar/glass areas (like the File Open dialog) and causes most button and tab controls to be unthemed.
Opus uses the standard Windows visual styles system to draw its UI so I'm not sure what you mean about Opus having its own skins. Yes, you can override how things look in some places (e.g. replace the background used by toolbars) but that does not cause any problems with WB, and nor should it. All WB is doing is intercepting the visual styles API and/or replacing elements of the theme, and Opus is fine with that.