The XP penalties are almost meaningless given how XP is scaled in this game. Even with the worst penalty possible you only trail a no penalty PC by 2-4 levels, which amounts to 20 skill points at the end of the game -- and considering the gigantic value some of the traits are by then, that's a huge loss. (Expect +9 to Magery, Blademaster, and Sharpshooter, in addition to the 20% armor, from Divinely Touched. Elite Warrior provides about +6 to Blademaster and Parry plus a lot of extra carrying capacity. The Mage/Priest skills provide about +6 to spell skill and +3/+6 to Magical Efficiency; Natural Mage lets you cast mage spells in encumbering armor, but most encumbering armor is unnecessary anyway.)
Good Constitution does not add to Hardiness, it adds to resistances at I believe +6% each. Given that resistances are calculated by multiplication and not addition this is not very useful. Nimble Fingers adds up to +4 to Lockpicking, eventually. They are not worth the advantage slot.
Also, never use Humans. Nephils and Sliths both get equivalent points in weapon skills that help them earn combat proficiencies.
Abhi, I admire your courage in challenging Torment like this, but you don't know all of the game mechanics. Read some threads here and listen to the advice you will hear instead of claiming you know best.