Both Fluckey and O'Kane wrote about using "decks awash." IIRC, Fluckey went in to drop off the train raiders with "decks awash" to facilitate launching the rubber boats. He also reported running "decks awash" for an extended period when searching for survivors from the POW ship, to make it easier to pull men out of the water. O'Kane reported running "decks awash" when on lifeguard duty for a similar reason. Fluckey's POW rescues were notably in fairly heavy seas, too. If these two gentlemen say they could run a Fleet boat with decks awash and not turn turtle, I tend to believe them. Of course, there can be endless shades of meaning to "decks awash", so we can't easily compare what Fluckey or O'Kane did to the analysis at
http://www.subvetpaul.com/Flt_Class_Sub.html. There is also a matter of degree between "decks awash" and "radar depth" and Fleet boats regularly used the latter. Check Fluckey, O'Kane, Beach, and Galantin for examples.
My personal best guess (and just my opinion) is that there is a point at which the analysis is correct, but that the R/L boats stayed as far away from that point as they could while still achieving as much of the desired effect as they could. Sailing around the ocean with decks awash does not reflect R/L practice, but using it tactically might.