if you've dealt with many 6.4 failures, you'll understand why the default go-to on stuff like this is a "new engine" quote. it's cut and dry and gets the truck back on the road ASAP
even if they'd found the freeze plug, you think they'd want to let the truck go without tearing it down to check the bottom end after the oil pan was full of water?
patch jobs often come back to bite REPUTABLE shops because when something unforseen pops up, and the cab has to come back of again (or multiple times) the shop loses money and the customer still isn't happy with the price and how long it took to get it sorted out.
with all the time, labor, and money in parts you're going to have in it, I'd yank the short block and go through it/overhaul it
just my .02