If the 5V requires only a small current, using a boost (or even a flying-cap converter) from 3.3V would give wide flexibility for the input voltage. For higher 5V current it could instead be a buck-boost directly from Vin, which would be more efficient than boosting from the 3.3V rail.
One challenge you face is the large input voltage range required. This has a profound effect on the DC-DC: the stepping ratio down to 3.3V varies from about 1.8:1 (55% duty cycle) for 6V to about 11:1 (9% duty cycle) for 36V. Why does this matter? It affects the inductor choice and switching frequency: the higher the stepping ratio, the shorter the minimum on-time becomes.
If you can step down to 5V instead for your bulk voltage, then make 3.3V from that, then these extents become 83% and 14% for 6V and 36V, respectively. This will allow a higher switching frequency. As it is, many DCDC's will run at close to 100% duty, so the lower input is doable even though the Vin-Vout overhead voltage is just 1V (some regulators will even switch to linear mode as Vin gets close to Vout.) Meanwhile your 3.3V gets to be a low-voltage input type, so possibly less expensive and able to run at a higher switching frequency.