Not a dog behaviourist, but here's my take.
If you've created a safe environment for him in his crate, then he could well be more protective of food and treats given to him in his crate, plus he's enclosed/cornered and has nowhere to take his prized food, so could be more likely to guard it. What's he like with food given to him outside the crate?
There are some people who take the view that you should be able to take food off a dog at any time, others see growling as perfectly reasonable (when it's over food) and simply the dog letting you know it wants to be left alone with it's food. I'm not saying the former is wrong, but it does often seem pointless, other than the human trying to prove themselves the "pack leader".
I had a dog that was very protective of food that he was given. He was fed twice a day and always outside (whatever the weather) and never received anything in the house - and we never had a problem. Yet he was able to distinguish between "his" food (the food he was given in his bowl) and food he scavenged, and would drop on command or let me remove chicken bones from his mouth when on walks.
Interestingly, he was way less food motivated than my current dog, Reggie, who will eat anything and everything, but never guards or shows no aggression around it.