Well the idea as currently in the PDF is that the city always starts with 1 district, thus 1 citizen token and that is moved to the one faction that is actually in power. Factions can have 0 tokens and still be valid and existing.
The purpose of the citizen tokens is, among other things, to track the size of the city and make sure the desired size is reached. If they no longer double for power that would then removed he need for the cumbersome "repeat district outlines to mark density" rule and the tokens would be placed on the map to show districts and district densities: aka where people live.