I'm not tracking right now, but used to. So I can answer your question with the caveat that yes it is a pain and I stopped doing it. :)

> sauces you make yourself? I often mix some different oils, mustard, seeds, miso, bit of leamon juice and spices… but weighting and logging everything will take 3x the time to do the sauce itself

Yes. The thing is that it also makes you aware of how much everything "costs" you in terms of calories. You become a lot more aware of how big a glug you give of that oil.

> 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 don't understand this part of your question.

> Leftovers nutrients decrease with time

My goal was not to be "accurate", but to lose weight. Overestimating slightly was in fact preferred. So this is not an effect I would have worried about.

> counting how much you take of a meal shared with others, especially when you serves yourself multiple time

You estimate. You know that the whole thing was X so if you eat a quarter of it that is 0.25*X.

> different species/cultivation methods like the rustic small and dense cucumber from your neighbor and the spongy one from the supermarket in January

Cucumber is flavoured water. Whatever is the variability in calories you can probably just ignore it.