I also originally thought exactly what sevvy said, that it would eat seals away but decided not to post that because on second thoughts I reasoned that if it's safe for carburettors then it shouldn't eat O-rings.
But on "third thoughts" the O-rings in carbs are specifically fuel resistant and I'm not sure about the ones inside the engine, or any other seals for that matter!
The black in the old oil could either be the oil mix from the cylinder walls that was burnt in the combustion chambers (being thinner I would imagine that it gets past the oil scraper ring easier), also maybe mixed with dissolved carbon from the top of the pistons/cylinder head,
or melted seal material

.
You could maybe confirm this if you could see inside the cylinders. If the tops of the pistons are nice and clean, you could deduce that the Seafoam had simply cleaned out some carbon, and all is well.
But as Slinky says, there will still be quite a bit of that old "Seafoam mix" oil in there, upto about half a litre I reckon.
I read here somewhere that some people tip their bikes right over on both sides at oil change time in order to get the last few drops out of the cam wells on the cylinder head.
Seems a bit much, but if you can do it safely it certainly couldn't hurt.
I guess my point is that I'd be worried as hell that I did some damage to the motor, and would be doing anything I could think of to either verify or deny that.