I fully realize the 3.5L NA has been out since 2006, and put in many more cars than you listed, 2007-2014 Ford Edge, 2007-2010 Lincoln MKX, 2007-2014 Lincoln MKZ, 2008-2014, 2008-2009 Mercury Sable, 2009-2004 Ford Flex, 2012-2012 Ford Fusion Sport, etc. A nephew of mine had an Edge, while my niece drove her dad's MKX. I recall vividly the coolant in my nephew's Edge going down in the overflow tank and I could not figure out where it was going in a closed system because I could not see it leaking. Not for that reason, but he sold the car shortly thereafter and I don't doubt it could have been leaking into the engine.
I've explained it before, my niece was driving her dad's 2008 Lincoln MKX in Santa Monica one afternoon a couple of years ago when I received a call, because at the time I lived near that area, that her car was smoking from the engine and I then drove there as quickly as I could. When it arrived at the dealer via a tow truck, the service advisor and I looked at the engine and noticed the coolant was nowhere to be seen and yes it was the water pump. The Lincoln MKX had less than 50,000 miles on it.
I agree that the 3.5L NA engine is reliable but with ticking time bomb in it, the water pump. I would not have a problem if when the water pump failed the most it could do would be to cause the engine to overheat, but what I do have a problem with is the fact it can leak coolant into the engine oil that could go undetected until such time it has caused irreparable damage to the engine. There have been several sites posting potential lawsuits about the water pump due to it causing catastrophic engine failure. I think many owners of the vehicles listed above are not that sophisticated and pay the bill, probably begrudgingly. I do think this will get much more attention with Explorer owners because they are used to driving vehicles to a 150,000 plus miles without exorbitant maintenance bills or being surprised by a seized engine.
You need to do more homework on this comment. I've had two Ford transmissions rebuilt, one at about 100,000 miles and the other at about 152,000 vs Toyota's/Lexus's that I've owned with zero problems that went more miles than these two cars. Most transmission shops will be very candid about some of the Ford transmissions of the past that were not very reliable. I have no idea how reliable the transmission on the current Explorer is or isn't, time will tell. I don't doubt they've been put in other Ford vehicles of the past, but again, Explorer owners may have different expectations.