I assume the long stem increases the likelihood it will be dislodged from the ear because it increases torque at the point of contact when moving. The first AirPods were much less secure in the ear than current ones. Reducing stem length may lower the risk of them falling out.

The long stem may have been a necessary but suboptimal engineering tradeoff to get the first version out the door. A lot of design tweaks have gone into making AirPods less likely to fall out.