Attach stone veneer evenly to irregularly shaped foundation
Answering this for others that may encounter a similar situation.
I spoke with contractors at the local contractor supply store, showing them the same info as I included in the question here.
Their recommendation was to attach the lathe directly to the tall side of the foundation, and make the scratch coat thick enough to make up the difference. Then, on the rear side (where the foundation is stepped down), affix the cement board (on top of any other required things like WRB) and then do a thinner scratch coat on that.
Whether this is perfect, I’m unsure. But, it seems reasonable and I don’t see many viable alternatives.