The Firaxis editor has an option "Auto Name" for cities, as a check box. I believe this will assign the name automatically from the city list when enabled, although this should be checked. Currently, this editor does not support that. It should for comparability reasons, even if this is likely a rarely-used option in scenarios.
Setting as minor due to the expected rarity of the case, lack of an error when it occurs, and the fact that the option is preserved when enabled and saved in this editor. Nonetheless, preferably it would be visible and toggleable.