There is a debate.... I hear it alot.... that using a rod from the muzzle can damage the crown of the barrel and will affect the accuracy of the gun. It's applicable to any gun, but I've heard it more related to rifles. However, how much it affects accuracy is debatable.... varying opinions out there. Where I hear it most is between very serious target competition type shooters, vs normal non-competition shooters. Personally, I've done it both ways and I've never found any difference in accuracy between the two guns.
Then the other, as mentioned, is that going from the breach end.... is safety... you can't put it in there if there's a bullet in the way.