I did like you have yours and tucked it behind the weather strip. I think it would be a real pain to try and get it to slide into the weather strip even though that would probably look a little better and protect the foam over the long term. But the stuff is cheap, $5 for a 20' roll which is way more that you need for both sides of the truck, even on a quad cab.
Yeah, if you could get it on the inside, that would probably be great as far as making the backer rod last longer but like we said, that stuff's cheap...lol. Especially for as much as you get for as little as you pay for it. I got more than enough left over for another new application for anywhere between now and this winter if I'd wanna replace it on an annual basis but another thing, even if you were able to successfully stuff that stuff inside the cavity of the weatherstripping, you'd probably have to readjust your striker bolts so your doors will shut...lol. I know, been there, done that..lol.
I haven't even checked mine in while to see how it's holding up to the exposure of outside but hey, if yours is anything like mine, the weatherstripping does a pretty good job of smashing the rod just enough to hide it from the sun's rays.