"Combat damage is the more proveable cause. There is no proof of how it sank, other than the hole in the forward near porthole, tested to be easily shattered by a rifled musket"

If that were the case how did they surface and use the Blue lantern to signal a successful mission as planned? Why didn't they stay surfaced after that to abandon ship if the Damage occurred during the attack? Why is there no evidence that the crew paniced and left their stations if the boat was flooding?

That is why the "Damage" is believed to be caused by a WW II depth charge attack by an America Destroyer searching for a U-Boat outside Charleston Harbor.

And as you said to have been able to have shot out the porthole during the attack would have been a lucky shot under the conditions. Not impossible, but certainly lucky. And with every Crime scene investigation some evidence that you find is not always what it would seem to suggest.