If the transformer is what I'm looking to protect, it stands to reason that I'm going to place the fuses on the supply side of the breaker, which in the vast majority of cases is the high-voltage side. Only in cases where the supply is from the low-voltage side exclusively, for example in a small isolated system where the transformer is used to step up the generator['s] output voltage for long-distance transmission to the load, would using only low-voltage fuses be of value. If the relative robustness of the connected system vis-à-vis the connected generation is anywhere near unity, fusing on both sides might be of value... but that's just on the face of it, as in such situations it might make more sense to set up the generator relaying to recognize the single-phased condition and separate itself from said transformer.
Hope this helps.
CR
"As iron sharpens iron, so one person sharpens another." [Proverbs 27:17, NIV]