Regarding your first point:
At the trench run, one could argue that they needed their weapons armed because hey look, there's TIEs shooting at us. You're in extremely hostile territory; it makes perfect sense to keep your weapons ready. I'd rather get there alive than get there fast.
The rest of the points are good though. Personally, I'm okay with the "closed S-foils = go faster" line of thought because I grew up playing the X-wing/Rogue Squadron games. I like to think the lasers need to be farther apart to fire for fear of overheating, which would cause them to explode. Then when they close them, they cannot shoot and the power from the lasers goes to the engines. But that's just me.
During the trench run they were specifically intending to shoot only proton torpedoes, so if closing S foils would have made them go faster they probably would have done it then.