Yes, you can make bigger charms at Dark Messenger. I think Phantom meant the charm boxes which are stackable Platinum Spirit and HP charms.
Modi drops (thankfully) a lot of platinum charms of each kind, but they take a lot of inventory space and make it so that a lot of times charms are left to disappear on the ground. And it isn't always feasible to run to dark messenger to convert to amethyst or ruby charms between modis.
If they were the stackable kind, would make it easier to collect all the charms rather than them going to waste.