Can't speak to the differences between the 3.5 ECO and the 3.7 because I've never owned a 3.7. And I have no idea if the 3.5 ECO in the Transit is the same, or programmed the same, as the 3.5 ECO in my F150. I can tell you this...I love the 3.5 ECO. I picked up my 2016 F150 in May of 2016 and now have just shy of 20,000 miles on it, absolutely trouble free. As with all my vehicles, my fuel data gets entered into an Excel spreadsheet that calculates actual mileage. Don't be fooled by what the vehicle's computer tells you - there's a reason a lot of people call it the lie-o-meter. Mine consistently reads 1-2 mpg better than hand calculated. My 2007 Quigley E350 with the 6.8 V10 has a lifetime average of 11.9 mpg according to the spreadsheet. My 2016 F150 Scab with the 3.5 Eco - lifetime average 20.9 mpg. To me, that's an astonishing difference considering that the 3.5 will flat run away from the V10, especially in the mountains. The 3.5 Eco is a lot like driving a diesel - most of the engine's torque comes on strong below 2,000 rpm; rarely does the truck have to shift going up a steep grade. It's the torque curve that makes the 3.5 Eco such a great engine - look up the torque curves for both engines and compare. Do you want an engine that will be singing at 4,000 rpm when going over a pass - or one loafing along at 2,000? Best part of all is if you do a lot of driving at higher altitudes where normally aspirated engines struggle. Those turbos pack in the air and it just makes me smile to drive over 10-11,000 foot passes with no appreciable loss of power.
Don't let the turbos scare you...I've owned diesel pickups for many, many years and never had any trouble with a turbo!