First to answer your question about the dealers estimate. It is a fair estimate. However Eternabond Tape is a better choice in my opinion, requires less work, & last 2-3 times longer than the sealant they use on the most RV roofs. Can be done easily yourself. If you search on line you can buy it for about $50 per roll for a 50' roll.
If your windows need to be resealed, there are some posts on here that talk about how to reseal the windows. I think to do it correctly the windows should be removed, then the sealant laid in between the wall & the window frame then reinstall the window. If you don't want to do the windows , get an estimate from the dealer with an explanation of how is going to do it. Any one can tape off the window frame and apply silicon sealant. So if the dealer suggests this & you are convinced that this all that is needed , do it yourself all for the price of a roll of masking tape & a couple of tubes of exterior sealant from Home Depot.
I have read, but have not seen, that some manufactures are starting to use Eternabond Tape on thier roofs at manufacturing.
Dan Sees, Full Timing in the MH & Part timing in a S&B In Hampstead, NC
2013 Winnebago Journey 42e, 2014 Featherlite Car Hauler 3110 17.5', 2008 Mazda MX5,
2008 Toyota FJ Cruiser