I know treats get abused and that too much of anything, even if it is good, becomes toxic at some point. Personally I'm always skeptical about things unless it is proven with animals actually being on the diet for several years without issues, and preferably over several chinchilla generations. Even more preferably is to have a good necropsy at the end of each generation. If something is safe it will prove to be safe.
For regular pet owners I'll always recommend things that have been long established to be safe even if it's a mediocre product. Typically their pets are companions and most pet owners don't understand how to monitor and care for pets if something does go awry which has led to chinchilla losses in the past.
For people who want to experiment I see nothing wrong with experimenting when there are good reasons behind the experimentation. Especially when the owner is well educated, understands the risks and knows how to monitor and manage problems that may result. It can lead to better diets and better health for everyone's pet especially when it proves to be beneficial.
For someone who is not informed the loss of a pet or complications, even if they are not related, may become so misinterpreted that nothing good will come of it. That could explain some of the flame wars you've observed.
I've read the LY chinchillas article. I absolutely love the photography. I think the content is good. Personally I'll feed my chinchilla a diet that is much more basic. He is healthy and at a healthy weight and maybe when he gets old and frail I'll have to add more in to coax him to eat more or increase his available calories. It's nice to know I have some good healthy options.
As far as tooth decay I don't think that's a problem in the long run if you give occasional treats. Chinchillas teeth grow rapidly so it takes a constant supply of sugar of cause problems. Diets that give chinchillas a constant supply of dried fruit (like popular deluxe diets) have been known to do that. Also there are owners who go overboard on treats and they are constantly giving them junk because their pets beg them for food and they have no self control to refuse them.
Things like giving your chinchilla your nut based snack mix every day with potato chips and that kind of thing does cause liver problems where fat will build up in the liver causing permanent damage. If someone like that had a dog it probably wouldn't be very healthy but that kind of diet is certain death to a chin. Lipidosis is scary because the damage can be cumulative.