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

To be safe with anything except a fairly new house, you’d need to excavate around the house, parge the outside of the foundation with asphalt, install a dimpled plastic membrane over that, and then on the inside, fastidiously install rigid foam on the floor and walls, spray foam/tape all seams, etc… Then frame, then drywall.Seems ungodly expensive.

As an old civil engineer I’m not confident that all those penetrations through shingles and membrane would stay water tight.  

We were told that there was pooling (flat roof) and that isn't good, but the membrane looked OK and should last a few more years probably.

Then apply a polypropylene waterproofing membrane over your work for added insurance. 

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.

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

The roof is in bad shape (1980s age) and is currently a spray foam and membrane type roof.  

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.