I mean, a new skill appearing on a list is still a new skill. I don't think it would be more confusing. I actually think the opposite would be more likely.
"Wait I'm on SCH," says the new player, "Why do I suddenly have this SMN skill? Is my game glitched?"
VS
"Oh, look a new skill was added to my SCH."
I think it's only as much work as you want to make it, too. It could temporarily reuse the same animation as Miasma or a Logos action but edited with a different hue. They could even copy and paste some enemy skill or Logos animation in - like how Fluid Aura's animation is literally just the Water spell animation enemies use. Either of these would cut development time by a lot.
The truth of the matter, unfortunately, is that unless it's already been a planned project, any change like this which requires rebalancing a kit won't make it in time for the next patch. Everything for 5.35 is already finished and at most is just undergoing some final testing. 5.4 has already been planned during 5.3s development and is being developed now - we already know MNK is seeing a massive rework for this patch and will suck up most resources for job balancing/adjustments. The earliest we would see anything would be by 5.5 which poses a tricky situation as BLU released in 4.5 and there are rumors of BST following that example for 5.5. But WHM saw it's big buff in 4.5 so perhaps SCH could echo that with 5.5 before it gets more attention for 6.0. But by that point the ends might not justify the means with an expansion around the corner...