So, there are some things that just dont add up or we are missing some info here
RECAP:
Coolant is low, you get an indicator.
You do not see an over temp indicator.
Restart you get a hard start, white smoke, engine noise and call a tow truck.
Visual inspection = engine coolant level is low.
Dealership states: fresh water in the cylinders and a cracked block.
Later post: you say they only found water in the intake.
Later post: you say they didnt pull the heads just the intake.
Dealership finds O'Reily air filters in the air box, not stock air filters.
Dealership cannot find the low coolant code in the computer.
Water in the intake: In the air box or in the blower? If water was found only in the air box, the box will need to be tested to make sure its draining correctly. A small amount of water in the box, does not mean you drove it into high water.
The computer would have set a hard code for the low coolant.
Dealership would not need to pull the heads to find water in the cylinder. Pull a sparkplug, look with a borescope and pull a sample. Did they do that?
Blocks do not crack from an overheat. Heads warp and crack from overheat.
Blocks crack, pistons crack and rods bend from hydrolock (cylinder filled with liquid). While driving, it is nearly impossible to instantly hydrolock you engine.
After you shut it off for the hour, a blown head gasket "could" allow enough coolant into the cylinder to hydrolock it.
Here is my take:
Assuming you did not drive it into deep water.
Dealership pulled the intake, found the aftermarket filters (no biggie).
Dealership found some fresh water in the bottom of the air box, and "assumed" you drove it into the water. From there, they didnt go any further and just "assumed" and reacted poorly.
If / when they pull the heads, they will find COOLANT in the cylinder, a blown head gasket and also catastrophic damage from a hydrolock even.
This is an exercise of forensics, not off the cuff dealer assumptions. Find a new dealer and have them take a look, it will be covered under warranty.
The only caveat is IF the new dealer finds fresh water in the cylinder(s), front diff, rear diff, t-case, etc. you are screwed.
Good luck bro and let us know!