The BD8152FVM integrates a FET, making external FET drive, and therefore step-up 55V/3A output, impossible. However, inputting IC drive voltage (i.e. 12V) to the Vcc of the BD9306AFVM controller allows for high input/output voltage operation.
The BD9006 features a minimum ON time of 250ns. For example, with a switching frequency of 100kHz the minimum ON duty ratio is 250ns/(1/100kHz) x 100 = 2.5%. So with an input voltage of 35V the minimum output voltage is 35V x 2.5% = 0.875V. It is possible to achieve the desired output by decreaseing the switching frequency. However, the inductor and capacitor values will increase.