100 is not so short that you won't get good weight loss. Sounds like he's just trying to ensure you don't get malnourished. In my case, the doctor said most of his DSs end up at around 75 cm. I asked for a bit longer to help ensure I wouldn't be malnourished or get diarrhea. So mine is about 85-90. It's fine.
Please remember we're literally only taking a few inches on a small intestine that can be 20 feet long.
In my case, I said I'd rather have a few extra pounds (if any) than deal with excess malnutrition, etc. As it is, I'm already mildly anemic, low in cooper and my PTH is up thanks to the DS.
Up to you, but what he's saying doesn't seem unreasonable to me.