Can anyone please describe with details? Where is it, how high on a stock bike?

Just wondering how deep would the water have to be for me to worry about mud getting into the CVT and having to open the cover to clean it out.

Second question... I assume the CVT has a little drain hole and it will only let water out, not in, correct?

It's just under your dash display. Air intake for the engine is a few inches lower under the "hump" between your legs.

CVT box does not have a one way valve as you describe, just a bolt with a crush washer that you can remove to drain in case you get water in the box. You put the bolt back in once it's drained.