I don’t know about that, I always thought it was your digestive system that breaks down protein into amino acids. The liver will sometimes convert amino acids to glucose, but that can happen with any protein source. Over consuming any food is probably not a great idea, but having a soy protein shake isn’t going to hurt unless you have some allergy. Especially if it’s isolate.
it’s the same thing with oils and fats, your digestive system should be able to break these down into short chain fatty acids and eliminate stuff it can’t.
I don’t worry about any of that as long as the majority of my diet is from whole foods, lots of protein, plenty of fiber, a variety of fats.
energy balance, a healthy gut, moving to work the lymphatic system and muscles should be 95% of the focus.