Yeah, I guess you have a point, it does seem hard to weigh that thing provided how big, fat, and enraged it can be. However, all Pokemon are required to have information recorded in Height, Weight, Footprint, etc. I always thought of how right after you caught a Pokemon, you input the information yourself, so I wouldn't know how the trainer would weigh this Pokemon by him/herself, but they most likely have some way of doing. After all, they have ways of being able to weigh other stuff like cars and trucks that might weigh a little bit more than Groudon. Just remember it is a game and not everything is supposed to make sense.
Also, Groudon weighs 2094.4 pounds.