I'm thinking it's a bug too. But I'm still viewing this as change in saturation, not opacity, seeing as the objects have the same 'see through'-quality before and after... I don't know whether that would be important in handling this bug?
Sometimes clients have called because they can't tell the difference between some of the colors due to the flattening, so I'm more careful in selecting hues with enough initial difference.
I'm looking forward to seeing if this has a fix in a future build