Not sure why you got those 6 and 3... When you put one point in an attribute, you get 4, whatever the attribute is, and for health and energy, it's 16 points.
Of course, if you wear some items that gives % bonus to strength and health, or intelligence and energy, those will actually increase. But 3, you might have mislooked
It's indeed quite counter intuitive, but I'd guess it's for:
- being able to give moire points for 1 for health and energy (well, it could be 1 = 1 for other attributes, and 1 = 4 for these)
- make it so the player doesn't have to choose too many points at each level up, as one of the goal of Brian Sullivan was to make it simple to enhance your character (hence why no customization at character creation for example, or the ability to undo puting points in skills while you don't close the window - would have been cool for attributes as well, put 1 in int by mistake with my Hunter
)