Where the rod is on the outside it is exposed to the elements and can rust or at least build up deposits. It is cleaner where it goes through the seal and gets covered in protective oil. So there is a clean end and dirty end. There is advice on here about cleaning it up before refitting. When I replaced mine there was a distinct worn groove on the push rod where it went through the seal so I replaced the rod.
Mine was the later one piece rod so I was replacing like with like but the revailing advice, on this forum at least, seems to be that you can replace the two piece (with ball bearing) with the later one piece rod. It is suggested that this lessens the ability of the rod to wobble about in the seal. I presume this will help with sealing and postpone wear. Whatever the truth of it Yamama moved to the later one piece rod for some reason. They must have thought it better in some way.
There is also a bush behind the seal which, if worn, is said to allow the rod to wobble. Also plenty of advice here too on replacing this. I wiggled my rod from side to side (oooer missus) and it didn't seem too bad (like I would know) so I didn't bother.
Hope these suggestions help.
Dave