Disclaimer: I have no formal medical or scientific education.
My thesis is that the calcium created by man-made processes is not the correct isotope to support the biological functions for which calcium is required and the granules of unprocessed calcium that appear in Granulomatosis are there because they are of the wrong isotope and end up destroying the ANCA.
According to this article calcium isotopes are what the body needs, not just the element, calcium. It must be the right isotope or the required reaction does not occur (emphases mine):
...Calcium is the most abundant metal and the fifth-most abundant element in the human body. As electrolytes, calcium ions play a vital role in the physiological and biochemical processes of organisms and cells: in signal transduction pathways where they act as a second messenger; in neurotransmitter release from neurons; in contraction of all muscle cell types; as cofactors in many enzymes; and in fertilization. Calcium ions outside cells are important for maintaining the potential difference across excitable cell membranes as well as proper bone formation...
How many different isotopes of calcium are there? These are the main ones:
Now, I can't predict the actual odds of the industrial processes used to make this calcium resulting in the correct isotope by chance but it must be agreed that it is extremely unlikely. But even if they hit that particular lottery once, there are multiple processes in use in different countries so it seems extremely unlikely that the suppliers are supplying the right isotope.
I have a family member with this disease. She is very health conscious and was taking calcium supplements when she received the diagnosis for Granulomatosis With Polyangiitis. She has continued to take the supplements and despite the buildup of these granules of calcium crystals in her cells her bones are quickly losing calcium.
Ironically, our mother's disease was attributed to overuse of talcum powder, which is from dolomite:
Dolomite has been found in the granules of patients (sorry, can't find the link yet):