Electrons chug along fairly slowly and so to get, for example, a bulb to light almost instantly when a switch is closed requires that many, many electrons are being delivered to the bulb at any one instant in order to achieve the required current flow. This is not difficult to visualize when we consider the thickness of the wires compared to the size of individual electrons.
In your capacitor circuit, the minimum theoretical limit on the number of electrons flowing into the positive battery terminal and out of the negative terminal at any one instant is two, that is to say in pairs. This then causes one electron to flow off of each of the top plates of C2 & C3 and onto the bottom plate of C1.
As I think you already realise, when a capacitor is charging or discharging, the currents in its two leads must always be identical to each other at any instant in magnitude and in the same direction, that is to say one current flows in and the other identical current flows out. This gives the illusion of the current actually flowing through the capacitor but in reality no conduction current passes directly between a capacitor's plates except for a tiny leakage current.
So in your circuit, when the switch closes, as with any series circuit the current at all points must be identical in magnitude and in the same direction. This results in a pulse of current flowing off of the top of C2 & C3 and on to the bottom of C1. The flow of charge results in voltage increases across all 3 capacitors.
So even though the tops of C2 & C3 and the bottom of C1 are at identical voltages, a flow of charge does flow between them when the switch is closed. This can be understood as being no different to a flow of electrons on to the bottom of C2 & C3 even though the voltage at that point doesn't change. This flow of charge has the effect of increasing the voltages across C2 & C3 as an identical amount of charge flows off of the top of C2 & C3 and onto the bottom of C1 increasing C1's voltage as electrons are removed back to the batteries positive terminal from the top of C1.
And so, the minimalist concept is that two electrons must flow in and out of the battery (in pairs) to cater for one electron being removed from the top of each of C2 & C3.
To consider a single electron flowing from the top of C1 back to the battery resulting in a single electron being removed from the top of C2 or C3 would result in C2 and C3 having different voltages across them which is not theoretically possible as they are shorted together although in reality there could be voltage drops across the finite resistances of the leads etc.
If you were to consider the concept of a single electron flowing from the top of C1 back to the batteries positive terminal then you would probably be forced into considering the concept of fractions of electrons flowing off of the top of C2 & C3 onto the bottom of C1 and I wouldn't like to make any further comment about the validity of the concept of fractional electron current flow!