I note several things about the document:
1) It is clear that all home made stoves are prohibited. They explicitly list home made alcohol stoves as an example.
2) Alcohol fuel is "not Recommended", but I do not see that it is "Prohibited", as home made stoves are. So it sounds to me as if you can use commercial alcohol stoves without violating their policy, although you will be doing something they do not recommend.
3) If you are going to strictly adhere to their policy, don't overlook "During transport and storage, properly secure chemical fuel containers in an upright, vertical position." :)) (Perhaps this was written by a car-camper, not a backpacker?)
That said, I am in strongly favor of cooking over wood fires, especially for younger scouts, as long as you are in an area where gathering wood and making a fire is an acceptable activity. My concerns are:
* If younger scouts are using stoves, they will never learn to build fires in adverse conditions.
* Doing non-trivial cooking over a wood fire is a skill that is only learned through practice.
Remembering back to my own Scout days, I have always been grateful we were never allowed to use stoves. The reason is that having to build a wood fire in whatever weather one is out in, and then use it, is the best (only?) way to gain real solid fire-building skills.
Yes, I know that doing so takes a lot of time. Yes, I know that pot black is messy. Yes, I know that everything ends up smelling like woodsmoke. I still feel that, in terms of skill-building it is well worth it.
I hope I am not stepping on any toes, but I believe that allowing Scouts to use stoves prior to mastering the above skills is short-changing their Scouting experience.
(Note: the above may not apply to certain Venture Scout activities -- ones where the trip, not skill-building, is the goal.)