To the OP, sorry to hear of the damage.
So how should one prevent leakage?
For the bolt holes, you have introduced a clean hole through the floor. You have cut through the inner ply, the wood frame, and possibly another ply. This also includes a wood - wood transition/spacing/hole. There is then a transition from the wood to the metal framing. If you are going through a tube frame, two more transitions. If going into a metal plate or "L" frame, another transition.
It seems difficult to ensure any sealant placed into the hole will not be removed when the bolt goes through.
Do you pour in a sealant as you are placing the bolt?
Do you drill a bigger hole ? Would an 1/8", 1/16", 1/32" bigger reduce the gripping power of the bolt? If the bolt head is inside the cabin/on top, how would that be done. If the bolt head is in the bottom, what do you do about the shaft/nut in the cabin. Would you still get an issue of the bolt rubbing the side of the hole, removing the sealant.
Do you epoxy the hole -- literally filling it assuming the epoxy will permeate laterally into the wood, then re-drill
Do you just assume that the exterior grade ply glue, etc will prevent wicking?
Do you seal the bolt openings? Chalk will fail over time eg drying, vibration. Do you use a sealing type washer like a silicon/rubber/butyl based product? Between the wood layers?
The OP appears to state that the base is a plywood layer over a frame with no second plywood layer. Assuming the wood frame was not treated prior to assembly with the plywood, the entire edge meeting the plywood is a potential point of failure. Under coating could fail. Should one be treating the frame prior to assembly? Or is a good waterproof glue sufficient to seal this area?
Does frame flexing cause issues as the OP stated ? Is this a reason to build a stronger - less flexing frame? Or should the cabin/box "float" relative to the frame, so as to reduce flexing.