Leakage Flux in a Transformer
No, any loss is a separate factor.

Leakage inductance is that flux which does not couple to the other winding. It is simply a few turns of wire on an iron core, that is not coupled to the other winding - exactly like a stand alone inductance.

It is not a source of loss per se. 

Efficiency of the transformer (energy loss) does not worsen. Reactance does not cause power loss. The effectiveness of the transformer is reduced for certain applications. For other applications (welding, furnaces, battery chargers, resonant convertors) is is an integral functional circuit element. 

Also, is the leakage flux a good thing as it reduces the fault MVA level?
There are many applications where tightly coupling to the zero source impedance of the grid would be a bad thing, and transformers are designed to have leakage reactance. 

In one of my first jobs I had to stack battery charger transformers. Whereas in a "good" transformer laminations are stacked EIEIEIEI, ours were stacked EEEEIIIIEEEEIIII to increase the leakage reactance. The point was to limit current.

There are of course two leakage inductances, one on the primary and one on the secondary. But they are transforemr coupled, so we can represent them as just one.

A transformer model would have to include all the myriad loss components, and eddy and skin effect losses from stray fields are just one (probably small) component.