Mutilate Skill Node within Puncture Skill tree

Does the node take into account the extended duration bleeds from the Penetrate skill (ie 30% increased duration) when it calculates the instant damage? Or does the node make all bleeds generic? (Ie a bleed caused by an item / other skill modifiers? Or does it segregate bleed applied from various sources then add damage together for total combined damage?

Not sure what you mean with the segregate part.

But the Greater Puncture does consume all stacks of bleed on the target (from whatever source they were applied).

And whatever the remaining damage of all the bleed stacks that were removed was, will be dealt as damage.

So this does include any penetration, inc. or more multipliers and duration.

Yeah, any damage that they would have done had they run their full duration is done immediately, however it’s still bleed damage (an ailment/DoT).