1. They were still present, whether you can agree they were majorly present or not is irrelevant. We still got a second version, it's totally plausible to happen here. It also happened with Gunblades.

2. None of what I propose is a retcon.

3. Red Mages in XIV only popped up in 2017, so you're off by about ten years. Every game does Red Mages (and really any job) at least a little bit different.

4. The lore book didn't say they're the same thing as Conjurer though. Using the same elements is not the same thing as being the same job. Again, we can just look at Red Mage, where it uses some of the same elements, same role, and even has a balance feature like Black Mage. That's a lot more overlap than a hypothetical Geomancer as, if nothing else, it's unlikely it would use lilies as a gimmick. Since Red Mage can be different from Black Mage Geomancer could be different from White Mage, especially when they don't even use the same elements anymore (and really two spells and a wonky ability is not the same thing as an entire job).