Gems that have been exposed to spirits can be used as magic crests/a prison that traps a flow.You'll note the wording of 'in particular' in relation to gems exposed to spirits, which is part of a separate thought from using jewels in general to store magical energy. Also why do you assume that a change in humanity's cultural perception of gems won't affect gemcraft?
Gee I wonder how that relates to storing magical energy in it.
Also I wouldn't say there's some huge mystery that's being encroached upon with putting magical energy into gems. It might be one thing if you're doing stuff based on say the seven treasures of Buddhism and such. But in the end you're mainly putting energy in the jewels.
For what purpose.Well that answers part of my question.
Should've clarified more though. I mean, how hard it would be for someone to forcibly take someone's magic crest?
You can put them in puppets or other things, you can dissect them, you can make butterfly wings with them (dumb and wasteful, but Touko does it anyway)
Spiritual surgery shouldn't be required as a speciality for it.