There is an issue with materials that have transparency or alpha clipping. I ran a quick test with custom shader, one having full transparency and another one having full alpha clipping. When running on visionOS the transparent object is semi transparent and it makes the object inside of it semi transparent too (it also could be that object inside of it is not visible at all. The object with full alpha clipping is fully visible.
I have already created a bug report about this, but it would be good to know if I did anything wrong or is there any work arounds for this