Google search reveals a lot of pictures of three-phase transformers. Looks like a common setup is to have three pairs of winding and a shared core. The core typically consists of three "bars" in parallel and each pair of windings is wrapped onto its own "bar" and the "bars" are connected on both ends so the core is closed and effectively it is one single core of complex shape and each pair of windings occupies its dedicated place on the core.
----------- << the two horizontal bars are free | | | | | | << windings are wrapped onto this vertical bars | | | << each pair occupies a separate bar | | | | | | -----------
Now as I see it each phase will induce its own magnetic flux and since each phase is offset by 120 degrees its flux will also be offset and those three fluxes should mix and more or less annihilate each other (full annihilation should happen when all phases are loaded equally) and so the transformer should not output any power on the secondary windings. However three-phase transformers work just fine.
How does a three-phase transformer work with magnetic flux of each phase passing through the common core?