Minecraft v1.12.2
Forge v14.23.5.2838
Custom Ideas v1.5.0.0
Tolkien Tweaks v3.0.7
Quick Store v1.1
Quark r1.5-168

With the above mods, the inventory GUI overlaps with the mods' buttons. The Custom Idea's Chest Button overlaps with the shield slot. The Tolkien Tweaks Milestone button overlaps with the hotbar, and the Quick Store Container button also overlaps the hotbar. It looks like the backpack inventory doesn't translate them like it does with the Recipe Book.
Is this fixable from here, or do I need to report this to each mod? Thanks!

Report it to those mods. They should allow configuration of this.

Alright, it has been reported to
brandon3055/Tolkien-Tweaks#1
ChampionAsh5357/Custom-Ideas#11
and to Quick Store.