Hardest part is kitchen and utility room have oak hardwood floor under existing old style linoleum and has to come out,,,replaced with 3/4" plywood,,,then Green E underlayment ,,,then I use a water barrier membrane then tile and of course grout.

Some will go with a nicer pad and a cheaper carpet.The nicer pad makes the carpet FEEL more expensive to the tenant when they walk on it.A great pad also resists wear and tear and if you need to replace the carpet the pad usually can be used again.Used to you would put a plastic membrane in between the carpet and pad to protect the pad but the plastic would slide and make noise sometimes.Now they have pads with built in protection.You are not looking for the cheapest product but the best VALUE for what you pay.It depends on the area and what kind of tenants and rent base you are working with.

Bottom line a roofing company isn't going to typically pay for punctures to the membrane of the roof like a roof mounted a/c unit.

I had a flat roof at my office that needed to be worked on every 4-5 years even after the promise of the installation of magic rubber membranes and all kinds of other crap.  

Quote from @Mark Coates: Whenever you install tile over concrete an uncoupling membrane must be used to isolate your tile/ grout from the possibility of a crack in the slab ruining your floor.

Well the original roofer sent out a helper who just kept plugging the hole (I think he came out 3 times) and it kept on leaking because it was a low pitch roof that needed a membrane and not shingles.

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

The plan though is to sell the house in two years and I wouldn't want to sell anyone something that wasn't built right,You would want to lay the concrete / cement below the leveler in all of the cracks (don't count on the leveler to fill them), then use schluter ditra below the flooring if you're going to use tile.Ditra is expensive but worth it - https://www.homedepot.com/p/Schluter-Ditra-54-sq-ft-3-ft-3-in-x-16-ft-5-in-x-1-8-in-Thick-Uncoupling-Membrane-DITRA5M/100143471Otherwise, based on the info given, I would focus on drainage and monitor the situation.  

It's time to re-roof one of our MF buildings and I don't have any experience dealing with flat roofs with torch-on membranes.