Travis-- Jerry from DIYAutoTune here.. Definitely make your own decision here, and there is something to be said for using a system your tuner knows, though the MS interface is extremely easy to use. Mac Spikes is actually running an MSPNP on his IT car, you could chat him up.
You're right alot of the guys running these are running boost, but that's simply as that's the forums we hung out on a bunch and borrowed beta testers from during development. That and we have a 250+ whp boost 91 Miata running an MSPNP. We also have a fairly mild N/A 95 Miata running an MSPNP. Both run great and the 95 picked up power with a good tune too. The 96/97 test cars we borrowed for that models dev process responded well too of course. Bottom line, it's a great product and the price is tough to beat. The base map is a great starting point, very driveable unless you're modded to the gills, and makes tuning a breeze. I have to agree with the above, tuning time varies with any EMS, and one of the biggest factors is how cool does it stay while on the dyno. In some cases (many in fact) you'll spend more time waiting for the car to cool down than you do tuning, that costs you money. I'm guessing your car has a fairly adequate cooling system though, and in general Miata's aren't that bad off in my experience. For the racer crowd that I know is running adequate fuel, I can even give you some pointers to end up with a very solid ignition map quick, only needing minor touch on the dyno. We have a Dynapack in house, and basically tuned the ignition map optimally, and then pulled 3 degrees across all load ranges from 2300rpms on up to redline. This was on pump93 fuel. If you're running pump93 or better you should be able to drop this back in and be 90% there, just letting your tuner fine tune from there based on the fuel you're running and your engines unique needs. They will of course need to go through your entire fuel table, but that takes no time at all.
Any questions... just let us know.