I had similar issues in 10.4, when trying to create a mining age. The requirements are really simple: Extreme Hills, Dense Ores, solid ground (no caves, water, lava etc.), no meteors, no decay. Surface effects like Hunger or Weakness don't matter, since I always dig down and set up the quarries at y55.
But no matter what, in 10.4 I always got caves, underground lakes, sometimes not even the correct biome.
Turned out, I made two mistakes:
1. I've used "No seas" as feature. This is in fact now a terrain modifier, so the correct usage would be something like "Stone Blocks, No seas, Flat" ... or don't use it at all. If used as a feature at the end, then it will ignore your original biome description.
2. The features are really goofy now. They fall into three categories: "Caved" ("Unknown" in the wiki, includes Caves, Ravines, Tendrils etc), "Nature" (Crystals, Trees, Lakes, Star Fissure) and "Civilization" (Dungeons, Mines, Obelisks, Villages). Seems, if you don't pick three each, then Mystcraft will add random features to it and cause instabilities.
Try out the following, this gave me the mining age I was looking for:
Flat, Extreme Hills, Single Biome, Bright, Eternal Rain
Zero Length, Noon, Normal Sun, Normal Moon, Normal Stars (or skip the celestials all together)
Stone Blocks, Tendrils, Stone Blocks, Tendrils, Stone Blocks, Tendrils (Normal World Gen still seems to work on stone blocks. If I skipped the material, then it always created wood tendrils under ground.)
Huge Trees, Huge Trees, Huge Trees (Crystals would be another choice, but it might add instability)
Villages, Villages, Obelisks (or any other surface structure, I was looking for the "cheapest" with the lowest chance of instabilities)
Dense Ore, Charged x 3, Scorched Surface x 3
Clear Modifiers
