So, I decided to go ahead and do a brake fluid flush on my 4Runner today and while it wasn't a "success" it wasn't a failure either.

So, I began by doing the basic hose-in-a-bottle setup and took out some of the brake fluid from the reservoir and put it in the bottle with a turkey baster. The fluid was definitely dirty, but not terrible. However, when I started on the passenger rear drain nipple the fluid that came out was actually very clean! I had my brother pumping the brake pedal and got a little bit out, but decided to switch to the other side, but couldn't get it to open (it was bright outside and couldn't tell if it was rusted shut or if the plug simply wasn't turning).

Rather than open up the caps on the front tires I just cleaned everything up, topped off the fluid, and went on a test drive and the brakes work well just like before. I poured through the previous owner's maintenance records and it did say that he had the brakes replaced back in 2011.

Still, I was very surprised to see how clean it was coming through the line even though the stuff in the reservoir was rather dirty. Is it possible that since the cap to the brake reservoir is just a simple rubber cap rather than a screw-on cap that over time contaminants somehow got inside the tank itself, but haven't reached the lines?

Just wanted some thoughts on it. The brakes work just fine so I'd rather not do any maintenance that isn't really necessary.

What you saw is normal: the fluid in the system that is most exposed to the atmosphere is that fluid in the reservoir, thanks to the system being vented to the outside(not sealed).
The big danger is that brake fluid slowly collects water out of the surrounding air(hygroscopic), and water plus steel brake tubing and hardware are, as you can imagine, a poor combination.

And lowers the boiling point of the fluid.... and starts boiling at 100 Celsius (212 F) due to the presence of water. The vapor will then fill the brake lines and at braking, the vapor gets compressed and as a result, no power is transmitted to the brake pistons to exert a force on the disk/drum to stop the vehicle.