I think I'm overall not in favor of this largely because of the negative listed in the OP. If I move to another continent, I might have tools I've earned taken away. Why are they taken away? Just because. It would be like going into a new zone in WoW and having your Hunter's Bow taken away. But the Warrior gets to keep his sword. Why? Why not.
I understand the desire to create a system whereby a player improves his character that doesn't feel grindy, but I don't feel this system does that. Look at it like this: In the current system your gems become worse slowly as the Civ level goes up. But in this suggestion your gems can become instantly worthless when your Civ level goes up. It kind of is like the current situation, but instead of gradual it is sudden, and instead of all gems, it is 30% of gems. That and you now can't just go pick up the gems you need, you have to find a mission that offers a reward of the gems you need to unlock.
So it kind of is what we have now, but 70% less annoying.