> - sauces you make yourself?
I don't count them. I keep my sauces simple and use them sparingly. I'm not trying to get down to sub-10% bf.
> - different cooking time in one receive : oignons going first, tomato sauce in the middle and parsley at the end (but still cook a bit with residual heat)
I count them raw, or if my tracker has them, count them as cooked. I don't care about them being super accurate.
> - Leftovers nutrients decrease with time
I don't care. The calorie counts are basically just estimates anyway. It's less a science than a mental game to control your ballpark calories in.
> - counting how much you take of a meal shared with others, especially when you serves yourself multiple time
If I'm making the meal, I count for the whole meal, then estimate for the share. See above for rationale (I don't care that much.) If my friend has cooked for me, I don't care at all, and just try to eat a "reasonable" portion.
> - different species/cultivation methods like the rustic small and dense cucumber from your neighbor and the spongy one from the supermarket in January
The differences are probably not going to matter all that much. By weight, a cucumber is a cucumber is a cucumber; I'm not trying to be perfect, just get a general sense of calories.