I came back to FFXIV last week and upgraded my Zenith to Atma just yesterday. It took me three nights of FATE grinding, so about 7 hours or so, with 3 hours of it just sitting in the same spot waiting for the same FATE because I found a nice online novel to read and didn't want to bother running after FATE spawns that night.

So the Atma step was nerfed severely, so much so that I'd say it was outright generous, compared to the horror stories I found while I was researching it.

I believe the problem mentioned in the op will be taken care of one way or the other when the time comes. The devs have shown that they have no qualms helping the latecomers move along.