The stronghold occasionally eats items (copper pendant is the most recent one) but does not provide a point bonus for them.
Several gems like phenelopes and garnets do not contribute to the resource total but others do.
Additionally, I'm uncertain if this is intentional or not, but the two dispensary / prestige items I put into the stronghold cost 5 each -- which seems perhaps suspiciously low considering their overall value?
For reference (I don't know if this is intentional) these don't work:
(https://i.gyazo.com/d944200b8757180d478766470682be80.png)
Gems never worked for me but I did not try ALL the gems.
Prestige items always yielded their proper value, some Dispenser prestige items are just the kings garbage.