Actually the goal is to have no medium lived isotopes. Long lived isotopes are simply not a problem, as their level of radioactivity can easily be low enough to be safer than the original uranium ore. Short lived half lives, will decay down to nothing in more manageable time frames.
Like if we had no medium half life isotopes, we may only need to keep waste safe for a few hundred years, perhaps 1000 at most, before remaining short lived isotopes contribute negligible radiation, leaving just the long half life isotopes. If those are long enough we have waste not meaningfully more dangerous than the original uranium ore, and can simply bury it.
A lot of this does depend on the specifics of input fuel and breeding cycles used, but there have been designs that would be able to reprocess any medium lived half-life outputs, leaving only reasonably short lived, and very long lived outputs.
The real question is what is the overall effect of such reprocessing on the cost efficiency. Presumably, breeder reprocessing entails some level of cost (additional equipment, additional monitoring, etc), and we may end up with some not completely optimal components in the fuel after reprocessing, which would mean lower operating efficiency. But by how much? How much less cost efficient doing the right thing here makes the plants is a critically important concern.