How does the Void Ray's Prismatic Alignment ability work with upgrades?

The void ray's new Prismatic Alignment ability increases the damage it does versus armored by 6 when used. However the ability also says "This does not scale with upgrades.". What does that mean exactly?

It would stand to reason that the void ray's normal damage of 6, with the prismatic alignment ability would raise it to 6+6=12 (versus armored), and that if you upgraded one weapon level to 6+1, that prismatic alignment would be (6+1)+6=13. If this is not the case, then the ability would become less effective the later the game went on. Since this is not a percentage increase against armored, what does the ability mean by "does not scale with upgrades"?

It is exactly as you say - activating the ability adds 6 damage when attacking armored units.

It's simply that this 6 "bonus" damage will always remain at 6.

The Wings of Liberty Void Ray went from 6 damage in stage one to 8 damage in stage two. Tellingly, the bonus damage to armored units also increased, from +4 damage in stage one, to +8(+1/upgrade) bonus damage in stage two.

Long story short, Void Rays with fully charged beams (now triggerable, with the ability) used to have their bonus damage scale with upgrades. Now, in HotS, they do not, so Blizzard elected to note this via tooltip.

Quoted from the site you have Void Ray under Balance Update #8:

Prismatic Beam:

No longer charges up.
Weapon period decreased from 0.6 to 0.5.
No longer does passive +massive damage. 

Prismatic Alignment (new ability) increases damage to armored units by 6 for 20 seconds, with a 1 minute cooldown. This does not scale with upgrades

Saying that it does NOT scale for upgrades. Therefore the bonus is just + 6, instead of a possible +9 (if weapons are +3).