There's something that seems totally counter intuitive to me.

When you're in low light and trying to shoot at lower shutter speeds it makes sense to get rid of the extra vibrations caused by the physical shutter, i.e. engage the electronic shutter instead.

However, when using the electronic shutter the max ISO is 3200, which means any benefit of the electronic shutter just flew out the window because you're forcing a lower shutter speed than otherwise possible.

Why would they put this limitation on us?

The same goes for flash - when the electronic shutter is enabled the flash is disabled. Why would they do that?

The electronic shutter isn't to get rid of mechanical shutter vibrations. It's to engage in a completely silent shooting mode.

Quality actually suffers with this turned on, so you should avoid it unless you need absolutely silent photo taking abilities.