The export is flattened yes, but each texture set is exported separately.
I hope in future updates, this will combine all texture sets. The current workaround is to create a mask using the RGB-A merge in Substance Designer, after painting a mask in Painter.
And blending the sets using a blend and a mask node. Actually, I do have a question in regards to fill layers... when we create a fill layer, why does the background fill with the color of the layer, unless this is done to minimise seams