I planted a few baptisias last spring and they did well. I went to look at them today and noticed they sunk into the soil quite a bit this winter. I topped them off with more soil. So now I am guessing the crown is 3-4" or so below the soil I added. Will they grow well planted that deeply?

They should be fine. They are very hardy plants.

The develop a deep taproot and spread here.
I doubt you will have a problem.
They are very hard to transplant.