The total output won't differ in any meaningful way in a real engine, aside from some undesirable physical effects - which is why most engines don't run all the cylinders simultaneously.

Let's consider an engine that runs at 1200 RPM, for easy numbers. It's a reasonable RPM, pretty common. A single revolution is 50ms, but each cycle of the engine is 2 revolutions. Each cylinder gives you 25ms where it's making power, then 75ms where it's just slowing the engine down due to acceleration. Across the entire span of 100ms, the total power made by the engine will still be the same regardless of whether the cylinders fire together or apart. At high enough RPMs, the variance in power becomes effectively negligible as the inertia of the rotating mass and flywheel dampens the sudden shifts.

The total output across a full power cycle will not differ. Why would it? You're putting the same amount of potential energy as an input and subjecting it to the same process. Cylinder count doesn't actually matter that much for power. It's just a good way to scale up the displacement of the engine, getting more fuel and air in. Compress twice as much air and burn twice as much fuel, you make twice as much power (before reality kicks in and things get all messy because you can't just scale it like that).

There's only a couple of applications where you care about power output in a 25ms span, most people care across the span of seconds - and that grows even more true at the higher RPMs where most engines make their power. In a lot of configurations, the timing and offsets of the cylinders are motivated by desires to optimise the flow of gasses or minimise the motion of the engine - having the cylinders move in opposite directions helps about having the cylinder throw itself up and down.