I don’t do this anymore, but when I was, the answers are as follows:

I didn’t make a ton of sauces myself, but if it was then I would round spices down to zero and weigh the main caloric components (think mayo, soy sauce, sugar, oil, tomato paste, etc)

I always weighed the uncooked food, so different cooking times was a non factor.

As for nutrients decreasing, I dealt with this by not believing in it. Seriously though, I was tracking fats, carbs, and proteins which to my knowledge do not meaningfully decay in non negligible amounts.

I lived alone so I didn’t often have to cook for multiple people. When I did I would just make 2 omelets or waffles or whatever and weigh mine.

As far as different species/cultivation methods, I realized there was an absolute edge to my ability to track. For example: bread is often listed at 70 calories per slice, but if you weigh each slice, you’ll find it deviates from what the package considers a “slice” of bread substantially. Further, you’ll often find packages that are inconsistent. For example, you might see a box that claims 14g of a food is 5 calories but the entire 28g container is also listed at 15 calories.