If you do the spire to the top frequently, it's not possible to burn through them all. I craft just about every cycle and still have over a million fragments.
There's no legacy involved.
Though my inventory is not as high as yours, with over 500K fragments in both cities I agree. It's almost impossible for 'legacy' to be involved in a feature that has only been available for a little over a year with the multiplayer feature only being available less than a year.
Please stop trying to reduce spell fragment rewards further.
I don't see this suggestion of a 'fragment store' as a reduction in spell fragments. It would be an option for spending them, not a requirement as I read it. There was a suggestion sent from here to the devs to have the fragments increased in the Gateway and High Halls and eliminated in the Laboratory so it would not adversely effect fragments for cities who find the Laboratory a drain on their resources. I don't think that suggestion was an overall reduction in fragments (if it was, it was not a huge reduction), but we have seen no indication they are seriously considering that suggestion.
I think the easiest way to increase fragment inventory is to place the moonstone libraries. In my oldest city I had 4 sets placed at one time, but have reduced that to 3 (and 4 more in inventory!) with all 4 link bonuses, so I gain extra fragments there. In my other city, I have reduced the libraries to only 1, but originally had 3 of them and that started the excess spell fragment situation there. I also craft every cycle and will use timers to craft more than one item/cycle when I want. I've set the cycle refresh time so I rarely if ever miss a cycle. Like almost everything else in this game, I view the Spire as a marathon, not a sprint. I've been reaching the top of the Spire each week for ~9months now in both cities. Hang in there! In time, I'd wager you'll be looking for ways to spend extra fragments, too!