Well, as of now, where "internal" Überhangmandate are possible, there is negative vote weight. Of course the mode of seat allocation could be changed to fix seat contingents per federal state (as in Spain or Finland for example). But this would not be a voting system not proportional as a whole, as the Constitutional Court demanded.
And if half of the seats should be given to the winners of single seat constituencies, as is the case since 1949, there would not be any possibility of compensation for the Überhangmandate. But the court demanded that 15 is the constitutional limit.
And there would be one argument less for the five percent threshold.
So maybe this easiest way to get rid of the negative vote weight, is not possible by constitutional restrictions and political opportunity.