The weights would be nearly identical. The only thing that would be mandated on a Trans Am would be power brakes and power steering. Power brake booster adds 5 lbs, p/s pump and gearbox unit is 21 lbs heavier than a manual box. Adding 26 lbs to the engine area, and 9 lbs for a rear wing, The extra 35 lbs. is not going to be measurable on a dragstrip.
The aerodynamics of the 69 Trans Am were not cosmetic, they were functional. The front spoiler would add about 1-2 mph in the traps by keeping the nose down and air out from underneath the car, the side air extractors would relieve underhood pressure, and the front/rear wing combo would push about 75 lbs of downforce on the suspension at 100 mph, lowering the car about 1 inch through the traps. On top of that, the larger hood scoop openings, placed at the leading edge of the hood on the 69 T/A, pulled in far more air than the small scoops in the middle of the 67-69 hood.
Like I said, it's nit-picking, because I know your point was really about the engines, but in the scenario you listed above, the 69 Trans Am would win at the dragstrip. In fact, it would also win at the Bonneville Salt Flats, and on a road course.
BTW, I don't own a 69 T/A, but I recently got into an argument on another site with a GTO Judge owner that thought the 69 Trans Am was "cosmetic", as in nothing more a "wing and a set of stripes". So I corrected him ("Defender of the Firebird" that I am) saying that in fact it was The Judge that was actually a cosmetic package, while the 69 Trans Am was a true performance car.