I suspect that a turbo will not increase your economy. Under very light part throttle driving, aka hypermiling, your manifold is under the same exact amount of vacuum as if there was no turbo. Think about your manifold pressure not in terms of vacuum, but in terms of barametric (absolute) pressure, where barametric pressure is approx 30"HG. At light throttle low revs you may have 5-10"HG (PSI = "HG/2) pressure. At WOT you may have 25"HG, or close to barametric pressure. Sort of backwards to a vacuum guage. Add a turbo, and you increase this pressure on top of what you already have. 10 PSI of boost gives you a manifold pressure (absolute) of 50" HG. This will only happen under heavy throttle, a state that we all try to avoid when we hypermile.
However, you may be on to something with messing around with valve overlap. You could possibly increase manifold pressure (ie, reduce vacuum) with an atkinson cycle and a turbo more than you could without a turbo. However, would it idle? In this situation, I suspect that a belt driven supercharger would be a better choice, because it would increase manifold pressure as soon as the engine started to turn over. I believe Mazda had a Miller cycle V6 that relied on a supercharger.
Miller cycle - Wikipedia, the free encyclopedia
Unfortunately, if this engine would have been a MPG wonder, we would all know about it and everyone else would have copied it. But they didn't.
The only time a turbocharged engine has proven to be an asset is when a much smaller turbocharged engine has been used with similar power of a larger NA engine that the car would normally be equipped with. Maybe this could be an option for you.