"the holes do not seem to want to line up"
With the pin inserted on one side, how far off is the hole on the other side? A quarter inch, half inch?
I know the hitch tube itself on my 2016 is a lot tighter than the one on my old 2010 Highlander Limited. Every dang thing I pulled rattled on the Highlander. Nothing rattles when hooked to my 4Runner, even my girlfriend's old piece of junk 5' x 8' 1-ton-rated trash trailer that I renovated 2 years ago with a complete wire brushing, Ospho treatment and a case of rattle cans of Rustoleum primer. And 2 new 14" tires from Northern on sale. Spared no expense.
I also have a 16' boat on a trailer, a heavy 2-bike rack, fold down cooler rack, etc., fwiw, so I'm surprised to hear there're 4Runners with problems (other than that goofy light plug location - jeez)