I don't see much problem here, since it doesn't make things any harder for the engines, only a little for the controllers. As Gunnar pointed out, there are hardly cases when engines would like to make any specific setup after `boardsize', but the undefined state was left mainly for consistency with undefined state at startup.
In any case, I believe it is way to left to change anything for GTP 2 except for _clarifying_ things. Since the draft has been out there for so long, it has become a de facto GTP 2 standard. If Gunnar ever releases the final GTP 2, which he has promised for more than a year now, I believe, it should be 100% compatible with the draft.
If GTP 2 is released, then we can think about improvements for GTP 3.
One thing I'd like to see is expansion to Game Text Protocol, which already exists (virtually), but is not documented anywhere. There is at least one Game Text Protocol controller (Quarry) and at least two non-Go engines: GRhino (GTP Othello engine) and two or three engines from never released Inge Wallin's set of game engines for Amazons, Othello and Lines of Action.
Paul