HPT does have injection timing control and ratio control for DI and PI.
HPT can program for ethanol (in Fords they are missing a sliding stoich table) spark lead adjustments, boost limits, etc. Without the sliding stoich table having the other flex tables doesn't really matter since you need to manually flash another file with a corresponding stoich value, but yes you are right, they don't have full flex capability for the ecoboost like they do for GM stuff (which is where they started) yet.
HPT does not allow access to the BCM or other modules due to legality/liability concerns, that is true. Not sure what I would do with ABS though, I like it.....I have never had an issue with this having tuned hundreds of vehicles.....?
So really, HPT needs to add a sliding stoich table on EcoBoost calibrations that will enable the use of all the other flex tables that are already there. The NGauge is what they chose to allow multiple tunes, I don't use one so I don't know if they are good or not....sounds like you don't like it, which is cool.
I just got the Gas Monkey Pantera traded in at my store with an SCT tune and it would not idle or run and was very rich, fouling plugs, etc. I don't know why it was like that, it couldn't have been like that at Gas Monkey..... I pulled the tune with HPT, made some adjustments, flashed it back on with HPT and now it runs perfectly. I use HPT on my 18 Raptor without any limitations (except flex fuel, I think multiple tunes are old school, ironically enough) and also my 17 Z06, and any other Ford, GM, Dodge, or last gen AMG someone wants me to tune.
Functionally speaking for creating well made tunes, HPT works wonderfully and I also like the interface and ability to set up the Scanner, etc compared to Cobb (which I have used on Subarus) and SCT or EFILive, I hate using all of those. I haven't tried ECUTek before, I just haven't needed it for what I do.