At first I was making fun of them, but joke's on me--the deer is surprisingly ergonomic, except for the kicks.
Standing desks are a current fad in modern tech companies. Supposedly more ergonomic and comfortable than sitting all day, they can be combined with treadmills or stationary bicycles to enable exercise to be taken while working. Cueball tells Megan that standing desks are inferior to his solution, strapping his laptop to a deer. The deer constantly runs away from Cueball, forcing him to chase and get exercise (and probably get kicked if he catches up). Additionally, by mentioning the common line of "humans weren't meant to sit all day", he is saying that his deer-based solution is much more similar to the task that humans evolved to do, namely hunting and gathering. Humans are in fact one of the few species built for persistence hunting, and are able to chase prey for more than four hours in ideal conditions. This is also why one's legs feel sore when standing for extended periods but not while moving.
The title text takes this a step further, saying that the deer was surprisingly ergonomic, apart from the kicks — which would, presumably, be quite debilitating. The ergonomics could be due to the soft, warm nature of the flesh compared to typical cold, hard tables.