There is no justification for the bunks to be set that high above the trailer frame. You want those as low as possible to avoid problems like you are having.
Launching a setup like this into knee deep water is never going to go well. To back in further may drop the trailer wheels off the edge of the ramp. While that may allow the boat to be launched, you could be in for a real battle getting the boat back on that trailer. If this is an unimproved dirt ramp, might be time to do some wading prior to another try. That rig is going to need waist deep water to float that boat.
The guy that told you smaller tires would blow due to weight needs to back into a heavy duty butt kicking machine. That boat, unless the toons are full of water or something else is going on, shouldn't weigh much more than a larger popup camper.....