I think you should hook to SkillTooltip or SkillTooltipTopLevel. I just tried like this:
Lua Code:
local f = SkillTooltip.SetSkillAbility
SkillTooltip.SetSkillAbility = function(self,...)
self:AddHeaderLine("test", "ZoFontGame", 1, TOOLTIP_HEADER_SIDE_LEFT, 1, 1, 1)
f(self,...)
end
and it displays "test" in a skill ability tooltip in the Skills window but not in the tooltip above the action bar.