Tbh, I'm not sure I understood the question of the TO.
If you want the "buff stack" number seperate from the ability level, you can always remove the actual ability buff and manually place a buff with appropriate level on the unit via triggers.
So, let's say your ability level is 10, but you want the buff to only show "2" in it's tooltip:
You trigger the ability, remove the default buff it applies and then add a modified tornado aura to the unit and set it to level 2 to make the tooltip display a "2".
... this will require you to fully trigger the effect of the buff aswell, though. So, for example, if you want an inner fire effect with customized stacks, you'd have to apply the armor and damage effect of the buff manually.
Then again, you probably already did this, since most default abilities won't stack anyway.
You need an endless amount of abilities instead.
You cannot do this without changing the icon of the ability.
Not true. Auras actually show a number next to the buff icon that displays the level of the aura.