There are pros and cons of building up with a crawlspace and not. With a crawlspace you run the risk of animals getting up there and nesting and creating holes and ruining the rubber. My biggest problem with EPDM (synthetic rubber) is ants. They make nice perfectly round little holes.
Building on top you won't have access to it. The idea of creating the deck in sections isn't a bad idea at all.

When you lay rubber down on something soft and poke it, say you drop a knife, the rubber will stretch and break through. If you lay the rubber down on something hard and drop the knife on it it will hardly effect it. That's why I'm with Tom on the fully adhered. Gluing the membrane down on a hard surface will make it more durable but it will drive up the cost. Plywood is expensive.
It will also make it a lot easier to find a leak, if it ever does.

I like the TPO for a membrane. It's heat welded together and holds up well. It's installed the same way as the EPDM.

I have never been a fan of modified roofs. I see here that people have had success with it but I have never seen one that hasn't leaked.

Danny

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