Apart from the general comfort of Lycra on a bike when you are really moving around to shift weight on the bike lycra is less likely to get caught on the saddle. If you are fully set up for downhill the saddle may be out of the way but for a cross country ride with interesting bits it can be much safer than baggies.
Bike-specific baggies are generally slimmer in the thigh and cut higher in the rear/crotch to reduce getting caught in the saddle. I ride mostly with baggies and it's not a problem I've ever experienced.
