I think that difference is fair, actually. It's MUCH easier to get a set of a UR in a mini-box than it is in a main box, and in your example, you'd only get 1 copy of each UR in the main box, but 3 from the minis. That's a very relevant difference.
I don't have much hope in Konami doing something to balance this out to make it fair. Idk if they have a new team full of greedy people, or if they are alrrady working on a new game and are trying to 🔥 this one to get it started on time. Either way, they will lose more players.