Just coming in to say I think you'll be fine with that set up. My in laws tow a travel trailer of a similar size/weight with their Sequoia and it does just fine.
On the bunks, what size come with it? Ours has really large bunks... about queen size, so plenty of room for an adult-size person. But if you really don't want them, I don't see anything wrong with asking to have them deleted. If for some reason you can't, it's easy enough to not use them. In our old bumper pull hauler, we never used the garage bed once, it just stayed stowed up at the top.