I have the automatic transmission so floor liners where not a problem. I first bought the Husky liners and after about two years threw the front ones away because the sides were folding in/warping catching your feet as you got in and out of the car. The sides of the Husky liners also started rubbing on the gas pedal, which was not safe. I then paid up and got the Weather Tech liners and they have been great.
As for the manual and automatic liner differences, I think the auto trans liner has a slight rise in the passenger side floor pan were the manual trans floor pan is flat on the passenger side. Don't hold me to that but I remembered something like that when I was looking for liners and read it somewhere.
I don't think there's a difference between the two cars. We have one of each and I'll have to compare them side by side. The only difference would be the extra pedal on the floor! As far as floor pan measurements they should be identical.