but when FB is below 400mV, it thinks its got an output short and goes into fault mode, discharging the soft start capacitor, also, if FB goes >1.25v, it goes into fault mode and stops switching?
Why do you want to use an IC designed to power LEDs and use it for what it was not designed for? It's hard enough to design switching voltage regulators using components designed for that purpose without throwing some extra unknowns into the mix.
It has an inductor. Most buck/boost converters also use inductors, not transformers. Still don't see a reason to use the LM3791 as a voltage regulator.