If you have the headers coated inside and out, the temperature drop in the engine compartment is dramatic. The way the shorty's go pretty much straight down from the center of the block requires new/modified head pipes, which will be forward of where the current pipes attach and farther from the firewall at the connection.
In other words, there shouldn't be much difference either way. You can always fit some double foil sided insulation(similar to the stuff in this photo from Speedway Motors) just under you carpet.