My dog trainer tells me I should feed my mastiff pups separatly at schedualed times, but they dont eat as well

I have 10 and 18 week old matiff pups. My trainer is very good and had accomplished so much with my dogs even at such young ages. She says I need to start feeding them separate at schedualed times, I had been letting them eat at will from one bowl set with the food bowls full all day untill 7pm. Well, I am trying this suggestion of separation and one of them isnt eating as well at all, and the other has no change. But the one just seems much more interested in eating when the bowl is shared and his weight gain has slowed. I know he will eat if he is hungry but he is a mastiff pup and I want him to reach his full potential size and I am concerned. Should I just go back to feeding them together? I wasnt having any issues with food agression or any thing at all, the trainer just thinks it gives me more controll to do it her way and the schedualed feedings make treats during training more rewarding. So, her new way or my old way?