Totally spaced off on the Welkynd Treasures, woops.
Long story short, as long as the mod is loaded before OOO and StarX Vanilla Vampires (and similar mods which make drastic alterations to interior cells with White Welkynd Cluster lights) there appears to be no serious issues, some of the clusters just aren't lootable. I could find no bugs, crashes or glitches introduced as a result of using the Cluster Treasures mod, in general or with regards to Dungeon related quests.
As for the mod itself, it's not terribly unbalancing, though it isn't terribly balanced either. As an example, the lowest form of stone you can find is Descendent. When these come with an Attribute or Skill enchantment, it is +7 (Consider the Base Ring of Attribute is +2). A bit high for a the lowest level. Similarly, the Elemental resists are a bit high (15%), while the Shield (5%) and Weapon enchantments (5 damage for Elemental, 10 for dmg HP/MP and 5-10 for the absorb x 1 sec) are more balanced. Fortify HP, MP and FP were also well below broken, coming in at 10 points each.
The added amount of Soul Gems I didn't find unbalancing, as even in the high 20's I was still finding mostly Petty and Lesser Soul Gems and Descendent stones.
Think I'll keep the mod active, I like acrobatic rewards.