I haven't quite got around to try this yet but I was thinking it over and was thinking it may prove a problem.
My rendering framework so far draws any opaque meshes first, the Z-order isn't considered important what with the depth buffer. After that "cheap" transparent frames are drawn, also in no particular order but at least after the opaque ones and finally I sort the remaining transparent frames by their screen depth so that a transparent object behind another transparent object doesn't get clipped by being drawn after the first one.
However if I'm to use instancing for transparent frames that would benefit from the latter approach... this would be a problem wouldn't it (since they're all rendered in the same draw call and as such can't be sorted in with other meshes)? Is there any good solution to this or am I missing some point to instancing which means this really isn't an issue?