I know this thread is old, but HPTuners finally added most of the tables for the 2013-up SHO and 2011-2014 F-150's around mid July 2016. My 2014 SHO is now tuned using HPTuners and pulls 16+ psi across redline w/ 87 octane, stock airbox with dirty paper filter, and there aren't any fueling errors. The maximum inferred air massflow is about 50.1 lb/min and using Garrett's formula for estimating horsepower based on massflow, that's roughly 474 hp.
I haven't looked at SCT for the SHO, but I heard there's more than 1 driver demand table. HPTuners is working to add the driver demand table (for terrain??) which is what Sport mode uses. Without changing that table, shifting into Sport mode causes the car to go back to stock boost levels.
Other than that, HPT looks like it is good to go for 2013-up SHO's. They were still working on 2010-2012 SHOs, and 2015-up F-150/Mustangs. They support all of these vehicles, but there are missing tables.