The reason you will get mildew on the tile in a shower is because the water is not draining or drying properly. This could be cause of the tile not being installed correctly with the correct slope on the tile floor.

Your engineer was basically saying that you have a high water table, meaning that the underground water is very close to the surface of the ground.

Granite counter tops are normally fabricated to a high polished surface that makes it easier to maintain.

No you cannot use a stucco mix as a mortar bed for adjusting the uneven concrete floor.

For an ADA shower you can’t have a curb/dam. You need a minimum slope to drain of ¼” per foot and no more than ½” per foot. You need a two part drain with weeps for the primary waterproof membrane to clamp to.

Xypex is suppose to waterproof the concrete. So in theory it should prevent moisture migration in the concrete wall to help reduce the possibility of efflorescence.

Some types of natural stone will tend to warp when they are subjected to moisture and then dries, and when they are subjected to high temperatures and then cool.

It could be that there are voids under those portions of the tile where they sound hollow. Hollow sounds are not a defect, but they could be a symptom of a defect.

The black stain in the water has to be coming from somewhere and caused by something. The question is where and what?

The CBC and ADA are vague and subjective regarding slip resistance requirements. There are quantitative standards for ceramic tile in ANSI A137.1 that prescribe a Dynamic Coefficient of Friction (DCOF) test protocol and a minimum requirement for interior, level wet surfaces.