At least one cooked breakfast was in the rotation since at least 2015 (that’s just as far back as I have paperwork, I believe it has been for many years). Crews have been waking up before dawn for a couple of decades, so this is not a new concern.
The spirit of the choice is probably to reinforce eating as a crew and preparing things together.
The Philmont program isn’t about developing “21st century least-effort backpacking skills”. It is about teaching Scouts to be self-sufficient and responsible for their activities. It is about dwelling in 214,000 acres of undeveloped land with some of the best scenery imaginable. Waite Phillips wanted Scouts to see the West as he did, on the ground and working for the privilege (it truly is a privilege). Philmont is the WHOLE journey, not just the staff camps.
The best way for a Scout to learn that there are potential consequences to decisions is to see a “less than perfect” (in the eye of the beholder) day. If you start cooking before dawn, you can be walking “at dawn”.
Cooking breakfast will not ruin a day, let alone an entire trek. Ask your Scouts their opinion WITHOUT influencing it by phrases like “wasting time” or other terms. How YOU and the other advisors frame things will affect how they see things.
On a shakedown, time cooking and cleaning a breakfast. It isn’t going to take more than an hour -less than that if you have practiced. Let that be a day you cook in the pouch if you are really worried about every minute. (The staff camps don’t inspect your trash bags to see if your empty pouches are clean and dry)