The term "undersized" can refer to height, length, weight, mass, bulk, strength. Just because you think it typically refers to height doesn't mean that's the case.
Joakim Noah is a good defender. He hustles. And he does have good height and length for a center. But he is absolutely undersized due to bulk, mass, and strength. He is a solid defender at center in today's NBA because the NBA is so devoid of quality centers. Look at the last two playoffs and you'll see where Noah gets exposed as he had to defend Perkins/KG and then an old Shaq. His defensive rating shot up from his regular season defensive rating. For reference, Dirk Nowitzki had a better defensive rating than Joakim in the playoffs last season. Noah still can get manhandled because he's light in the ass and simply not strong enough.
He's like Marcus Camby. Tall, long, above average athletically. But you match him up against a real center with real center size and he'll get handled. And something I mentioned earlier will always be a problem for Noah. He has a thin upper frame. He lacks broad shoulders that could allow him to bulk up adequately in the upper body. It's something physical he can't do anything about, just like Kevin Willis' short arms. Noah will always be thin and not quite strong enough in the upper body. Like Camby, he can play center against a lot of the other centers in the league, but he's probably better suited to play power forward, since he has the athleticism and agility to keep up with a lot of power forwards and he can play more weak side help defender from that position.
Noah isn't the perfect complement to Boozer. The perfect complement to Boozer would be a player like David Robinson. A guy who can play the high post on offense but is very good defensively in the low post. With Noah, you have two power forwards, both of which offer different liabilities on defense against the elite front courts of the league.