GTO,
There will be some efficiency to gain, but I see a few hurdles.
One, even if your furnaces have combustion blowers, they are still draft furnaces requiring certain flue attributes as described
HERE. Be mindful of the requirements of other devices, like water heaters, that share a flue. You wouldn't want to create negative draft conditions that might invite carbon monoxide in the house!
If you lower the flue discharge temp, you are likely to get more corrosion of the flue since more condensation will occur and the flue won't be as hot at shutoff to reevaporate it.
You probably aren't going to take an unacceptable amount of heat away from the flue with the short section you describe, but you will certainly change the air/fuel ratio of the furnaces, since they will be drawing through a restriction instead of free air, and the inlet pressure your furnaces see will be lower still as the combustion air is trying to rise out of the inlet since it is now warmer and buoyant. The same volume of air now has fewer molecules of oxygen since it is warmer. If you do this, be sure the furnace runs at stoichiometric under all operating conditions.
Lastly, you will gain WAAAAYYYY more efficiency by relocating equipment and as much ductwork as possible into conditioned spaces (even building a conditioned space around them), or replacing with more efficient systems if you can. There is a frighteningly large amount of air leakage in equipment casings and air ducts, plus so much surface area to lose/gain heat through even if it is well sealed.
I removed both my furnaces and installed hydronic retrofit heat plate warm floors powered by a 95% efficient water heater, plus a 23SEER Nordyne inverter air conditioner which can vary its output from 1.5 to 3.5 tons, allowing one unit to cool the whole house. Rearranging the ducts to do this got all my equipment out of the attic and reduced the amount of ductwork in unconditioned space by half.
Even though I was now heating/cooling 3 floors AND a garage instead of just 2 floors in a 5br/3.5ba house, the cooling demand for kwh went down to 15kwh/day from around 60kwh/day, and my gas use during heating season went from 300-350 therms/mo to 175-225/mo.