If there is any air in the unit it will not be felt like the brake as it never "hardens out", typically air in the unit means less push from the cylinder, less push on the rod means less clutch action leading to possible cluncky initial gear selection.
As a side, mine is like that from cold, definitely clunky until it warms up then its smooth as silk.
My MPL has zero bubbles in it, and I don't seem to have the problem with seepage through the master cylinder either.......my oil does not go black anymore ever, but I do now change it annually (Not that that made a difference before).