Hi,
The tool left a safety margin of 25%. I would leave 33% safety margin.
It's a matter of choice. The higher the margin, the safer but most likely, the higher the cost. You can choose a safety margin you want buy I recommend not to go below 25%.
The better the layout, the less is stray inductance --> the less overshot. Thus you need less headroom.
The slower the voltage rise and fall rate --> the less overshot. Thus you need less headroom.
With a good layout 5V of headroom is enough, with a bad layout even 100% may not be sufficient.
I think the voltage rating of Q1 is more critical as Q2.
It's not just about the layout. You can have a very good layout and hope it will be fine but with a high closed-loop Q-factor, you'll still get large overshoots and lots of ringing.
Partially. It depends more on the conversion factor. It's better to make the selection at worst-case operating point and to use "identical" switches too.
It's okay. But components go bad in a circuit. You don't want the entire system dead as soon as one component goes bad. I think you need some more safety margin.