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The transmission in the ecoBoost will support a bit more than what you listed. Its the engine that is the weaker link. Push it too far and you get the "window mod" in the side of the block.
I ran the Mpt performance tune on my 2013 eco. The truck was a monster, I would make sure to data log and work with them to fine tune things to get the best results.
The truck had 60,000 miles on the tune and still ran great.
to answer your question/concern concisely: mpt tunes are not known to be harmful to the f150 transmission. i never had any issues running their race tune. your transmission should be fine (unless of course you are reckless in hos yoi isw your truck).
How long does it take to switch between tunes?
The Cobb accessport I had for my BMW was a pain in the **** to switch between tunes, it would take 30-45 min