Yeah, it's the stock tune only.
This would be nice functionality- along with being able to read tunes on the PCM and upload/modify them.
It really seems like no one self tunes in the Ford world compared to GM world where EVERYONE self tunes. I don't know if SCT's limitations are a cause or effect of this.
If you have the SCT handheld tuner, you can make adjustments to your aftermarket tune. Spark timing, air/fuel ratio, rev limit, axle ratio, tire size, fan turn on temps, etc...
The reason SCT doesn't allow you to read, download, and modify tunes on the PCM is because if you could do that, then one person could get a custom tune for their modifications, download it and either sell it or give it out for free, basically putting tuners out of business or hurting their business.