That drain is a typical clamping drain used with a liner. The Tile Council of North America (TCNA) handbook is the industry bible. They call for the minimum thickness of a mud bed over a wooden subfloor to be 1.5" (although many go thinner at the drain, but usually still 1" or so). There is no way the liner should be flat on the floor to meet industry guidelines or the plumbing code.
The plumbing code requires that the waterproofing be sloped to the drain. Neither tile nor grout is considered the waterproofing. The tiled surface is sloped because the material underneath it is, but to get that to happen, there's three layers:
- a preslope
- the liner
- an equal depth setting bed (i.e., parallel to the preslope and liner)
To save time and effort, it's not uncommon for people to omit the preslope. Especially if a plumber is called to install the drain. Otherwise, you need the tile guy to make the preslope, then call the plumber, get the flood test for the inspector, then the tile guy back to finish things up. What tends to happen if you've got a good tile guy, is the plumber installed the drain and the liner, tests it, then the tile guy tears the liner out, does a preslope, and puts it back in.
There are numerous ways to make a shower outlined in the TCNA handbook. None are particularly hard, but they are very detail oriented. If you follow one of them, you'll have a reliable, long-lasting shower.
Water WILL get beneath the tile in a shower pan. It will percolate down to the waterproof layer, and if it is properly sloped, it will slowly drain out, but nominally, be constantly damp. It's a first in, first out scenario. If the liner is flat on the floor, water will tend to accumulate and stagnate. This can keep the grout wet, and promote mold. Properly mixed deck mud is quite porous, so water will move through it. It's not particularly strong for abrasion, but is in compression (the tile cap it, so there's not an issue).