I don't think that the re-use of geneseed will have any type of 'filtering' through being used in multiple Astartes. Each Chapter has to send a tithe to the Mechanicus, so if any issues come up with the geneseed in general, or even a particular zygote, then it can be corrected; either it will be replaced completely from the stocks held in cryo-stasis, or thrown-out and a new geneseed/zygote will replace it. To my mind, any deterioration in the efficacy of the geneseed in creating Astartes is due to the process of implantation on initiation. This has become mindless reptition and the actual science of the process lost to ritual. In fact many of the rituals used will have a detrimental effect on the neophyte, meaning that the outcome will less than optimal. (I believe I read that in the IA on the process of making Marines.)
So, again to my view, geneseed-wise the 40k Astartes will be just as functionally immortal as their Great Crusade-era counterparts. Any differences will probably be slight and probably not noticed because most Astartes die in combat before any age-related issues become apparent. I would imagine that the issues with geneseed/zygote deterioration will be more pronounced in some Chapters- there will be those who don't really care about the science, they just want more Marines; there will be those whose Apothecaries will take a very great interest in what, and how, things are going on and so will have less problems, not needing the Mechanicus to keep re-supplying them with new or repaired geneseed.
As for older marines stepping out of combat roles. I could easily see this as being some sort of sabbatical. The fluff for Dante talks about how he is feeling the ennui of having lived so long, having seen everything and done everything, repeated hundreds or thousands of times. Even for biological weapons, Astartes still have something of their Humanity, and the sameness of combat will start to tell, dulling thier minds and making them bored. Once a Marine gets to a certain age they are probably made to take an extended break from their main role; maybe they go to teach the Scouts, maybe they step aside from leadership and allow someone new to be blooded, maybe they take on a research role in the Apothecarion or Librarius or Reclusiam, or even go on to a diplomatic role between other Chapters/Guard/Administratum or even go out with a Rogue Trader.
TL;DR I think that Astartes are still functionally immortal, except for those from Chapters whose implantation procedures have become debased; combat, however, will still be the primary (and hugely more common) cause of Astartes death. Old Marines will be made to change jobs regularly to keep them mentally fresh which would explain the fluff instances of Marines doing things other than being part of a Chapter's combat strength.
Phew, that was a long, rambling one!