Why is transformer higher voltage primary usually closest to the core and has the shortest loops?
For "concentric" wound transformers, I find both ways of them to be used, and the factors influencing it are most likely (may not all apply to your case):


Cost of the material involved. Higher current needs thicker wires, but the same number of turns (and even thicker if its on the outside because it is longer there). Just calculate what is needed for the number of turns required in either inner or outer layer, and then do a comparison. It seems to me the higher the step down ratio, the more beneficial it is to keep the high current ones inside.
Tapping. A lot of transformers have multiple tappings. Precise positioning and space for them is a lot easier on the outside than it is on the inside.
Serviceability and failure modes. Bigger transformers are actually so expensive that it might be feasible to repair them. Depending on the expected failure modes putting one or the other winding on the outside is more useful.
Rectangular cores might need different material strenghts and properties since internal forces are higher than in circular cores. Aluminum might be better suited here than the softer copper. This applies of course only at rather high currents (that are distributed unevenly in the conductor). Metal fatigue considerations however might drive you away from aluminum here.


Note that I don't call them secondary/primary but low/high voltage sides, I think those factors are more influential than the direction they are used in.