Having overpowered weapons with easy access to them isn't a part of any other sandbox game, including any of the ones you named. There isn't a holy iron battle-axe of the gods +500dmg that you can pick up in the beginning of Skyrim with people telling you "don't use it if you don't like it." Yet you're using sandbox as an excuse to justify having unbalanced mods together.
First of all, it is not a mod's job to be "balanced" in most cases. A mod cannot be unbalanced or overpowering in the absolute sense. They all torque and break vanilla and that's the only universal reference point.
So your argument is, "Xeno's Reliquary is unbalanced in this pack (DW20/Ultimate) because the holy hand grenade is super strong!"
I ask you, 'Who cares about strong weapons?" Already
many of our mods trivialize the wither battle. Most everyone already has nano suits, sabers, vanilla enchants, forcefields, deep holes, and other tools that basically make the wither a simple fight. The challenging of fighting the wither is not really the actual fight with the wither, it's making those wither skulls farmable. And the hand grenade is much less useful versus the only other "boss" of the game, the Ender Dragon. Already with vanilla mechanics I could one shot every other monster in the game. Tinker's Construct is coming into our packs, and that'll make it even worse. Ars Magica is coming into the DW20 pack, and you will not believe how strong that can make you. A well-decked high-level mage can fight someone in a gravity suit to a standstill (and their infrastructure has a UU-matter equivalent).
So yay. The hand grenade is very strong against a boss who's chief difficulty has always been, "Can you spawn him in?"
I heard a similar set of complaints from another user here, Vermillon, and as far as I can tell people have very weird ideas of the balance that exists in our current packs. The handgun: very good. But not insane. The potions: good, but much more expensive than vanilla potions for the same effects. The Alchemy system? Doesn't really change the game unless something comes along to change that balance. Now, when you combine any two Alchemy/Exchange systems and they aren't on the same page, it creates infinite resource loops. Right now EE3+XR means infinite resources (particularly if you have Xycraft fabricators to accelerate
the process to tick level speed). But again, who cares?
Infinite resources? Oh no. It's the end of the world! It's not like frame machines didn't already trivialize all of that. It's not like computercraft, ender tanks, and quarries couldn't be combined to give infinite resources. It's not like Ars Magica can't make infinite resources. Go play with MineChem and freak out at what you can do.
The only real rule of game and pack balance should be, "Does this totally obsolete every other option available?" If it does, then it shouldn't be in that pack (and possibly not in that mod). An example of an overpowered mechanic: Forestry's Bronze creation. Everyone else makes it harder to make bronze, so it's sensible to turn off the cheap bronze creation because no one will ever use Greg's bronze or Tinker's Construct's bronze methods; they're just much more time consuming.
tl;dr: XR's hand grenade is more balanced than Forestry's Bronze. What will you do now, internet?