Taking a TE in the third round is typically the correct move in terms of VBD. However, VBD does not take into account drafting your best team, only isolated situations from round to round that focuses on drafting the best player.
Taking a TE that early is a mistake, especially if you know who to target in later rounds who can produce at a level similar to the TE you take in the 3rd.
Maybe the TE you take in the 3rd outproduces my TE I take in the 9th by 5 points per game. But the WR or RB I take in the 3rd instead of the TE (and the subsequent trickle down effect of other players I take in the 4th, 5th, 6th, etc. rounds) will more than make up for that difference.
Your premise is incorrect. The idea that a TE taken in the third round will downgrade your WR, QB, and RB is no more correct than the idea that a WR taken in the third round will downgrade your QB, RB, and TE. The idea is true as far as it goes, but it's not really meaningful. Taking a TE with a VBD of 100 is better than taking a WR with a VBD of 70; you will not make up those 30 points later, because the VBD available in the fourth round will be the same whether or not you took a TE.In the common case, you'll optimize the VBD in your starting lineup if you take the higher-VBD player regardless of position. There are edge cases where this is not true, but Gonzo-in-the-third is not one of those edge cases. Gonzo outproduces your seventh-round TE by more than Reggie Wayne will outproduce a seventh-round WR.
Real-world example: By Antsports ADP, Gonzo is being taken just ahead of Reggie Wayne in the third round, and Ashley Lelie is being taken just ahead of Dallas Clark in the seventh. FBG projects Reggie Wayne for 1200/11 (187 fantasy points) and Ashley Lelie for 990/7 (142 fantasy points, 45 point difference). Gonzo is projected at 1080/8 (156 fantasy points) and Dallas Clark for 644/7 (106 fantasy points, 50 point difference). So in terms of absolute points, Gonzo is ahead. But in terms of fantasy value, Gonzo is even further ahead, because Gonzo's reliability is much higher than Wayne's or Clark's, and Lelie's upside is higher than Wayne's.
It is more likely that Gonzo meets his projections than that Reggie Wayne or Dallas Clark does. And it is more likely that Ashley Lelie produces as much as Reggie Wayne than that Dallas Clark produces as much as Gonzo.
Edit to add: FBG has Dallas Clark projected at 55 receptions. He had 25 last season, and Marcus Pollard had 29, so they are projecting Clark to get 100% of Pollard's receptions. It might happen, but it is fairly unlikely. The Colts under Manning have never had a 50-reception TE. This just points out that your seventh-round TE is a fairly marginal fantasy prospect.
Any way you look at it, Gonzo is a stronger pick than Reggie Wayne, who isn't even the #1 WR on his own team. And I would continue along the same lines and say it would be foolish to take Andre Johnson, Javon Walker, or Joe Horn ahead of Gonzo.