Well if you're flexed you're really lined up as an "H', or H-back. By the way I'm not making a case for or against the pick of Funchess, that wasn't my point. But just last year the Jets took Jace Amaro in the 2nd round, he was an (F) tight end at Texas Tech. Always lined up in the slot as a WR.
I think it's a better idea philisophically to take the more traditional tight ends early if they're a threat in the passing game. You don't have to deviate from your base personnel. You can play 'em inline or split out. It less predictable what the guy is going to do if he's inline, or lined up in a traditional (Y). They don't know if he's going to block or split the C2 down the seam and gain 30 yards. That's what makes a guy like Jason Witten such a weapon for so many years.