I tend to agree with you in theory that transparency seems like it could play a useful role in distinguishing active windows/apps, but in practice it is hard to use it effectively, as both of the cited examples tend to prove! :)
Of course you can play around with this a little yourself, either with the for-pay WindowShade, or the free InvisRay
http://www.davidestes.net/.
Anyway, this is stuff out of OG's control, and they don't really have many options, so IMHO the best option is 'greyed out' toolbar buttons, as noted before.
It's pretty simple to do, so I figured I's test it, and IMHO it seems like a workable solution with minimal effort and negative impact (you can still differentiate unavailable buttons/controls in background windows.)
You'd also want to have lighter drawer thumbnail icons to help avoid the confusion when a background drawer appears to belong to the active window.
The other most visible element that would help to highlight the active window would be to reduce the opacity/fill of the page thumbnails in background tab drawers, which would be a much more visible indication of the active window.
The argument can be made that this is non-standard behaviour, but there is an evident issue in the UI conventions with denoting the active window, made even more evident with the Unified Toolbar theme (which is otherwise superior IMHO, offering a larger drag target, and reducing visual noise in the toolbar.)
I tend to think of this as an extension of the existing convention of greying out window controls and titles, or OTOH that convention is incompletely implemented, and should already have been extended to the toolbars.
Any thoughts?