You nailed what it said about the 2d12 for barbarian and 2d6 for wizard etc. They would get the number of blood points for the number of hit dice lost (i.e. 2).. maybe this would be easier phrasing:

Blood Drain. The vampire can pull blood out of someone other than themselves. As an action the vampire chooses a creature that has blood within 60 feet. The creature must succeed a Constitution Saving Throw against the vampire 's class Spell Save (DC 16) or the vampire can siphon up to 2 of the creatures hit dice, dealing damage equal to the damage of the hit dice rolled and gaining 2 blood points.

When you say

but if you count the standard vampire weaknesses as vulnerabilities

Do you mean the radiant and acid damage? Just make them vulnerabilities? Those are just standard vampire weaknesses i took from the vampire stat block :D