Substats already are in effect at the minimum ilvl.
They already have values correlating to the gear we had at the time, that gear didn't just stop existing.
Balancing Nightmare is not true. They don't make a significant enough difference to make classes "impossible to balance", you're WAY overstating the effects of substats in lower content.

If job damage output is so vastly different at 50 than it is right now, you can do literally what I said, put an invisible %buff/debuff on the class at that level when doing minimum ilvl content to retain some semblance of balance.
Its not like its actually difficult to figure out how much damage a job would do at those levels to a point that would be considered reasonable levels of balancing. If a job like RDM is doing 200 more dps than NIN in 2.4 Shiva, nerf it by like 12%.
Its not actually important or breaking anyone's immersion when old min ilvl job balance isn't literally perfect.

Scaling the substats down or even damage output down is something they only have to do once per set of level cap, and not even to a perfect degree. The "balancing nightmare" here is blown way out of proportion. You literally do not have to adjust all of these abilities, you only have to adjust the actual output of a given class. There aren't any abilities we have that trivialize the content more than we are going to trivialize it anyway with it at level 80.