A rule of thumb (i.e. not exactly right!) I learned in my transformer design days, was that the leakage flux in a given winding is the flux that would be present if there was no core, or other strong coupling to the other windings. Leakage flux is the magnetic flux that isn't well coupled. Like an air core inductor wound just like the winding in question. Each different winding in a transformer will add it's own bit to the total leakage.
You can (sort of) think of the EM fields as a superposition of the with and without core cases. Adding a core both creates lots of additional flux as well as coupling it to the other windings, this will not eliminate the flux that would be created by the "air core" winding that would exist without a core present.
Of course it's not all about the core, although that is a common approximation. It's about possible flux paths that don't couple to the other windings. Transformer designers that care about leakage flux (good or bad) will pay a lot of attention to the geometry of the windings to control the area that is (or isn't) common to the other windings.
Finally, practical transformer designs are often very dependent on requirements in addition to the basic physics; like safety standards, cost of materials, reliability, or manufacturing issues. This is an area that is either dominated by practical experience (the stuff that you only learn in industry), or by computer simulations of very specific field configurations.