Howdy and Welcome to iRV2.com
Its great to have you here, many of us Started in tents then moved to a pop up. Cheri and I have had 2 an old Viking in Alaska and a Coleman Bayside (Fleetwood). We loved both but needed more room to carry the goldwing.
I don't see anything wrong with treating the bottom, I am sure it is treated but adding more cant hurt. I would also use RTV or Caulk around any seams while your under the camper. As far as the trunk leak goes I hqave heard of a few and if I recall they sealed around the seals also and I know I had to tighten the top on mine because it didnt close tight on the seal.
I just turned the latch1 turn at a time until I couldnt lift the lid.