Ultimately, the discounts and buffs are calculated differently based on where they're set.
Discounts (such as 50% cheaper upgrades) are set on the server, and override the previous values, while buffs are applied one-at-a-time based on your local progress. I would imagine there could be a "Factory Unit Buff Weekend" event, that would cause buffs to function in the same way discounts are factored. I'm not sure if this is something the design team has considered yet.