It's definitely an aftermarket panel for the climate control, but that's a necessity if you want to replace the head unit because the center panel is all one piece. It's all plug-and-play and shouldn't cause any problems. I drive my Mustang year-round and personally wouldn't be able to live with a touchscreen for climate controls because I need something that works when I'm wearing gloves, but YMMV.
If you have your heart set on a V6 manual you may not have much choice in the matter -- those seem to be pretty rare.
2013 GT Premium 6MT. GHIG, Black/Cashmere 401A interior, Comfort Package, 19" 5-spoke wheels. Two boosters, one RFT card for my parking garage at work, daily driver.