I must have read for days on this when I was installing mine, as well as talking with Tru-Cool. Those people really need better tech support because it took a miracle to get through to someone who knows anything about their products. There's some guys who think the only way for them to work is if the fittings are on the top and those who swear it doesn't matter. I looked at what Tru-Cool said, the fact that like you said the factory one works like that, the fact that there's plenty of guys who report that it works fine either way, and how my lines are coming into the bottom so it would be a PIA to route them to the top, and mounted it with the fittings at the bottom. And guess what? It worked great. But them a few months later I had to move it to behind the lower grill area because my intercooler needed to go where it was and the lines ended up at the top. It still works great.
Edit: I have a 2800 stall and a 4l60 level 3 "invincible" Performabuilt trans that cost me a small fortune so I wanted to be sure. Plus the blown and cammed 6.0 pushes it pretty hard. It stays cool.