Do nutritional facts take into account the inedible parts of certain foods? I was wondering if the caloric values of leftovers of certain foods (may the best example be bones, when eating chicken) that are never eaten, taken into account when calculating nutrition values of prepared meals. Most importantly when vendor/food outlet is obligated to put them on the packaging/leaflets.

I can't find a paper with detailed methodology of such calculations nowhere in the internet.
Nutritional values are based on Servings, not on the whole product, so it is realistic to assume that the values are based on what is actually to be consumed. 

As for the second part of your question, I would refer you to this site that simplifies FDA labeling and nutrition requirements:

https://www.foodpackaginglabels.net/food-labeling-requirements/