Exterior is stucco, roof is flat and clad in an elastomeric foam membrane (one of my biggest issues).  

The whole inclusure would need a membrane under floor and all wall tiles.

NASA lives at the whims of the white house's plans for space travel (that prospect looks like it is picking up) Take me with a grain of salt since I am brand new to this and just starting to look but I'd be happy to answer anything i can. 

A contractor or inspector can tell you the problem.You can use a backer board or rubber membrane but that will only mask the problem.

You may not always want that job and need to plan accordingly.15% is a common budget for maintenance.CAPEX budget can vary depending on the age of the systems inside and outside the buidling (does it have a parking lot, is the roof rubber membrane or asphalt shingle, do you have a boiler system or furnace, etc., etc.).Hope that helps - I'm sure there are others I didn't mention.

I believe its going to be about 1500 sq ft (currently a 2 layer in place)Suggestion for basic 10 year warranty roof is 45 mil EPDM Rubber Membrane. 

Are you tiling a shower or tub, if so another expensive area due to waterproof backer membrane.

i would paint the surface with any membrane like the one use in bathroom to prevent any of the pop corn falling off , then i would dry wall the whole area, good luck 

For example, if your roofing subcontractor did not properly install the weatherproofing membrane under the roof, leading to leaks, which damage the walls and floors, a liability policy would not cover the cost of repairing the roof, but would typically cover the damage to the walls and floors.While, you may be able to limit liability through through the contract terms, and an "as is" clause, (and I would consult with a lawyer in your area who knows what is allowable in your jurisdiction), that is not a substitute for a good liability policy.

But I wonder if they are being used for weight to keep the roof membrane down or something.