Where is this written as an option?
To my knowledge and to the extent of my google-fu, boneworking is not something ever used as a skill in PF. If your group or GM has made house rules which use it you'll have to ask them how they work as I can't tell you.
I've never bought into this in the past because I've never seen rules for this craft skill anywhere and I've only heard the above information one time from one person.
The most common Craft skills are alchemy, armor, baskets, books, bows, calligraphy, carpentry, cloth, clothing, glass, jewelry, leather, locks, paintings, pottery, sculptures, ships, shoes, stonemasonry, traps, and weapons.
My guess would be that this player, seeing that there was no fixed list of what you could learn to craft, invented a new craft skill and persuaded his GM that he could use it to substitute for necromancy components.
Crafting bone weapons and armor? But yea where did you find this? First I hear of it.
I don't think it did come from a Pathfinder book, at least not one made by Paizo, Dreamscarred Press or Drop Dead Studios. HeroLab might have added it themselves, possibly after playing Dwarf Fortress (where it gets used for practice/hunting crossbow bolts).
My search-fu only came up with homebrew: Arch Necromancer: The Darkest Art. This listed boneworking as a Craft(X) possibility.
/cevah