The latest and greatest products are paint on membrane systems that allow for a very waterproof building envelope.

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

***NOT taking off the old shingles, is only saving you around $1K (give or take)... if you're already going through all the hassle of new system, bite the bullet and do it correctly.When you remove the old layers, you can then: do any necessary repairs; possibly install ISO boards (insulation boards) smoothly; install the good membrane (not simple felt!)

Everything passed except for the "secondary roof" which consists of a membrane roof over an unheated, patio "room" separated from the man house by glass sliders.

I suppose even a 1/4” layer of sound dampening membrane is better than nothing, but why on earth would replacement of the entire subfloor be required?  

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.

If it is a tub or shower surround, make sure they are also installing a proper waterproofing membrane, otherwise you will be ripping it back out in 5 years.

.- Additional subfloor (wood) and cement board (floor) $100- Shower cement board $75- Waterproofing Membrane (I like to do this) $150- Shower wall tile (80-90 SF) $150- Flooring tile (30-40 SF) $100- Tile setting and grout $75- Vanity with top and mirror (24" it looks) $250- Toilet, wax ring and feed line $100- Faucet, feed lines and trap $75- Trim $25- Accessories $40- Fan/light $150- Vanity Light $50- *Shower diverter valve with trim kit and plumber to install and help set tub/drain. $750- Screws, adhesives and fasteners (cement board screws, caulk, etc) $50- Paint $40- Miscellaneous $100TOTAL: $2530With all of that said these numbers would be my BASE run, and assuming I was spending my budget amount on each item.

My installations on plywood or OSB subfloors are on HardieBacker and waterproofed with paintable membranes -- I built the tile floors in my rentals like shower stalls walls.

Then installing plywood back over the framing, new waterproof membrane, and new siding on the outside of the house.