In my opinion is all plain simple.
Apple don't offer upgrade price for products that ship with every new mac: OsX and iLife.
On the other hand it offers two prices (full and upgrade) for products that does not ship with every mac: iWork (yep, also if this isn't a pro app), and all others pro apps.
This lead to the point: Apple consider the price of iLife and OsX as upgrade price since every mac user have iLife and OsX.
Upgrading, Why It Hurts To Be A Mac User