Haven't made an extended trip in the JL, but took our JK from Houston to Vegas with one dog on the way there and two dogs on the way back. (we picked up a Weimaraner while we were there) Made our way back by way of the Grand Canyon and other parts of Arizona. I think the Wrangler Unlimiteds...
Soft top, no leaks.
Have always had water come in at A pillar on all my Jeeps after a car wash or a rain when opening the door.
One of the reasons I always have a couple of towels in the Jeep.
That and wet dogs.
Guessing someone had probably opened the passenger side before you.