If Iam going for synchronous rectification ( MOSFET is used instead of diode), would the gating pulses be same for both outputs?
It is through transformer turns ratio, we are able to adjust the output to different levels.
If the sync rectifiers are not synchronously gated then the body-diode of the sync rectifier MOSFET of each winding will be in conduction for different durations thus the advantage of sync rectification will be lost, partly or fully.
Wouldn't the driver need extra current capability for driving 2 switches in this case?
Yes. Apart from cross regulation and output voltage shifts, this is one of the main problems of multi-output converters with sync-rectified secondaries.
Assuming the controller is in primary side, can I transfer a single gating pulse across the isolation barrier and use it for both the o/p rectifier switches?
It's possible but you'll still need a separate voltage source or secondary-side aux winding to drive the MOSFETs and the driving problem mentioned above will still persist.
In multi-o/p converters, Is it possible to have one output as synchronous output and another output as non synchronous? The reason being I want the main output (Output1) as of high efficiency whereas the Output 2 (low current o/p) can be made non-synchronous.
Yes. The idea behind sync rectification is to decrease the losses due to the diode forward drop. You can go for sync rectification for the heavy output(s) and diode rectification for light output(s).
Now I'm imagining that if it would be beneficial if there was a smart sync rectification controller which tracks the output loading (i.e. load current) and decides when to turn the sync rectifier MOSFET on. Because using the body diode of the sync rectifier MOSFET at no load or very light loads would be less lossy compared to driving the MOSFET.