Own a 2013 4Runner Limited here. Honestly, it sounds like with your intended use an SR5 4x4 would be just fine. Even though it's not a Trail Edition once you put some new AT's on it, it's still plenty capable. You could probably get an SR5 Premium (has softex heated seats, sunroof, side blinkers, nav, etc) 4x4 for about $35k and the SR5 Non-premium for $33k. For my money I would probably get the Premium version though as I like having a sunroof. It's not a rock crawler by any means and wouldn't compare to Rubicon but it would be much more comfortable in long road trips, better pavement manners, and have more interior refinements than a Rubicon. As well you could build it up as much as you want to your liking. The benefit of having the Trail version is the rear locker, crawl control, and optional KDSS. If I could buy again, I'd probably just get an SR5 Premium 4x4 and with the cash saved put it towards mods.
The side cargo windows do not roll or open but the lift gate window rolls down electronically with a switch near the shifter. It can be left partially open or fully open to your desire.
As a previous 2007 Tacoma DCSB Pre-runner owner, I can say I really love driving the 4Runner and for my use it's an upgrade in every facet. I think you'd be happy in one too.