I think I know where the issue lies.
Steam usually doesn't have a problem when companies sell their games on an entirely different platform for cheaper.
What they do have a problem with is when companies try to use Steams' infrastructure, but not pay for it through the commission fee.
That's why it's illegal for companies to sell Steam Keys for their product on non-legitimized sites. The game would still use the Steam Workshop, Community Pages, Updater. Everything that is the actual things that cost the distributor (Steam) money.
In this case: The game is F2P on Steam. You only can't play competitively without DLC. So someone would download the game for free on Steam, enter UPlay for the secondary launcher, then purchase the full version on UPlay, because it's slightly cheaper than the Elite Edition (Retail: 20€).
As it seems: Usually when you buy a DLC through the external launcher, it would sync the DLC to Steam. Since you launched the game via Steam, giving Steam their cut. But because it is not available on Steam at all, Ubisoft gets to keep all the money, while still using Steam's infrastructure.