I don't see why. Getting enderpearls from iron always was a time saver, because you could always go hunting them in the night in the Overworld, so what changed after you set up your farm, besides the fact that you now have overflow of Enderpearls? In fact, the whole point of EE3 right now is being a time saver. Oh, i need 3 diamonds. Oh, wait, i know! I have 12 gold here i can burn. Bam. Done. No need to go mining for 10 minutes to actually go and find the three diamonds. Also, using it as a space saving measure. Overflow of gold? NP, save a barrel's worth, convert the rest to diamonds, turn into diamond blocks, store into a barrel. Convert back if you need to. Overflow of iron? Same deal. Don't want to waste precious time mining Obsidian (which is easily made, but is time consuming to acquire and mine)? NP, you never need much anyway, just transmute some logs. It's ALL about saving time, and compressing stuff into more valuable forms that you can convert back if needed. I don't see anything inherently OP about that, because in the end, it's all stuff you could've gotten yourself by mining, you're not making it out of thin air, like could do in EE2.
Like someone pointed out in another thread, you have a problem with infinite iron/gold? This is doable in vanilla. Iron Golem farm = Infinite Iron. Pigman Farm = Infinite Gold. Sure, the pigman farm is slow and laggy as hell, and you have to build dozens of Nether Portals, which take a lot of obsidian, which takes a lot of time to mine. And iron golem farms require handling villagers, which is tricky and time consuming. But in the end? Not like it's giving you anything besides what you could have gotten yourself, infinitely, and legitimately.
Now, if you were to say to me that Minium Stones have too many uses for the resources and the time it takes to get them, i'd agree. They should be nerfed so as to not allow them to be used so many times, so you'd still need to lose a little bit of time either making a good mobtrap, or hunting a lot of mobs, to keep getting shards of minium. But what they do? It's not OP at all. Being a time saver is not being OP, if it's just saving you time. It's when you start getting stuff with close to zero effort, that things start getting into the realms of OP, but right now, the only thing i know of that is able to do this, is UU-Matter Solar Factories, that keep producing more and more HV Solars that power mass fabs, that produce more UU, until you're drowning so badly in UU that you simply don't need quarries anymore, and keep running and getting more efficient as time passes with no input from the player after the first HV generates. But by the time you get there, you already have so much infrastructure set up, that it doesn't really matter anymore now, does it?
And even then, the UU Solar Factory is a contraption in my opinion, not an exploit. You're using the tools you were given, in a way they were intended to be used, only, the process is automated. Instead of crafting everything yourself out of the UU matter, it's all automatic...