When Tiffin seals the windows, they use a bead (tape) of butyl all the way around the underside of the outer flange of the window, so it will be squeezed against the outer sidewall when the window is inserted and tightened down. They then run a bead of silicone at the window/sidewall joint, but this doesn't go under the flange very far. The silicone only goes over the top and part way down the sides so if any water bypasses this first seal it is free to drain out at the lower part of the window. If you decide to do it yourself, use a flexible razor blade to cut the silicone and then clean the residue completely off the both surfaces. After the window removal, be sure the butyl is also thoroughly removed.
All that said, since the rig is still under warranty, let them do it. Just watch closely so you know the tricks for next time. I had to pull the driver side window to swap our Nevercold for a residential refrigerator on our 2008 Allegro Bus. Window removal and install is not a hard job, but it can be tedious, and the double pane windows tend to be heavy.
2013 Tiffin Allegro Bus 43QGP
2011 Chevy Silverado 1500 Toad