I don't have a current SEPST calibration listing on hand so can't say with authority, but I'm thinking the list of calibrations for that bike is entirely populated with EPA-compliant (which doesn't necessarily denote "undesirable" in and of itself) files for Harley-only parts combinations. Harley doesn't make a "true dual" exhaust for that bike, so no matter what else, they aren't going to have a base calibration that will be suitable-enough to just run it. You could install the closest one they have and run a few smart tune sessions against it and get it definitely close enough to use for breaking in the engine. That's what I'd do.
If the SEPST is still unopened, I'd take it back and get a TTS kit instead. Very much more capable in terms of engine tuning and there are other facets where it shines much more brightly. The only downside in comparison is that with the TTS you have to lug a laptop or netbook/tablet along while DIY datalogging. But the flipside of that is that you can obtain much better datalogs even if they're only 15 minutes long like you can do with the SEPST by itself. You can lug a computer along with the SEPST, too, and take longer data collections, but so far as I know your only option for data sets gives you 1/2 second sampling intervals (only 1 in 10 possible data points captured @ 2400 RPM). In terms of the "professional" tuner maybe not being familiar with TTS (proper), hopefully they've been doing it for a couple years anyway and should be familiar with the old SERT, and if so, they will immediately recognize the TTS software interface and should be able to jump right in with both feet.
The notion that the tuning interface to use is the one the tuner is most familiar with is only valid to a point. What if they're most familiar with the PC-III or PC-V? You're not going to be able to run closed-loop at all with the former and with the latter it's another several hundred dollars and more stuff to stow on the bike, effectively permanently, if you want to run closed-loop. But even then the ECM itself will be running open-loop and will therefore provide none of the learning adaptability it came with from the factory.
No, the learning the ECM can do is not suitable for adapting to different breathing parts. Well, maybe a high-flow air cleaner or more-open mufflers after the in-header-cat, but still not ideally. Think more in terms of different fuels you'll pick up over time, your fuel pressure regulator (or pump) getting tired over time, or your injectors having good days, bad days, or just old and tired days, etc. Even if the bike ran "okay" on whatever "close" calibration was in the ECM with different breathing gear installed, the adaptable range won't be fully available, at least in places, for its intended purpose any longer.