I suppose on this issue, I'm splitting hairs, but your question is a very good one. Microcrystalline hydroxyapatite is (or should be) a naturally occurring mineral form of calcium apatite, which is a constituent of bone matrix and teeth. If the source is the apatite, then this will be metabolized by the body naturally, but if a vitamin company uses actual ground bone for the source, then it has already been processed. This is when you purchase your products from a reputable, organic-type vitamin company, and buy the brands where the source is natural as opposed to cheaper sources more mass-produced vitamin manufacturers typically use.
To find out the source of any element or compound in your vitamins, you can contact the manufacturer. Sometimes the larger companies don't even know, but your smaller and more natural companies typically know what goes into their vitamins.
Egg membranes are good source of nutrients, and your company that uses this appears to be a good one. Egg membranes are a grey area - they are not a "by-product", in my opinion, as much as a living membrane supplying active nutrients. They are a "boundary."
You are seeking the best sources for your supplements - good post!