A rubber seal on the air duct in the marked section could potentially stop water intrusion at that connection point. It is one of the things I will be testing when I get my truck back.
It's because the TB has a factory lift. All configurations of the Silverado use the same liners. Sealing the connection should be enough to mitigate the risk of water intrusion, I just prefer redundancy when it comes to preventing this from happening again. Crafting an extension for the liner should be pretty easy and inexpensive.
We examined another truck with the same air intake configuration that went through the same water I did without issue. The differences between the 2 trucks were that mine is a TB with Mud Tires and his is an RST with street tires. The fender liners on the TB are higher relative to the tires allowing the water picked up by the tread to be thrown/pushed up and forward into the lower engine bay around the air duct. From there the air moving through the duct into the air cleaner acted as a syphon,drawing water into the air cleaner around the somewhat loose fitting duct.
I just had this happen last Wednesday. What kind of tires do you have. What we found is that the mud tread on my tires was throwing water up around the duct that goes into the air cleaner from the splash guard. The water was getting sucked in around that duct because it's not a sealed connection. I was driving through 6-8 inches of water.