If you stand a OEM axle and a new napa axle on end and measure them the napa one is always shorter. Mainly because they still "sucked" together inside the cups from when they make them. They do move and fit just fine once you get the axle half inside the transmission.
Don't forget that the threads are really long and will have more than enough sticking out to thread the nut on. Also you better make sure you get the correct one because the passenger side has 2 different part numbers. GT and GTP's have different length axles. I'll dealt with enough napa axles to know the new ones seem "shorter" out of the box.
Replacing the seal is pretty easy, screw driver or a chisel bit and smack it from the bottom to bend it up, then use the screw driver or yank it out with a channel locks or something. New one goes in with a large socket to keep it even.
