While I dont use MODFLOW-6, they probably decided to follow what was done with MODFLOW-NWT. I think conceptually it is fine.
I think it might lead to problems for "convertible" layers with the Newton formulation because--at least in the MODFLOW-2005 variant of NWT--cells
never really go dry because veritical conductance is held constant at the confine value. You could have a situation, where the GHB is below the bottom of a convertible layer which then pulls water out of the model from the surrounding cells, where traditional
MF-2005 would just set the cell to IBOUND=0 and disable the GHB.
Its very semantic, but you might see if the GHB works for CONFINE layers or not using a newton formulation.
Hope that helps out
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