you won't grow a 1-grain city to level 5 because you'll need >20 butchers across your empire (when you have them, who cares about a single city anymore?) and you'll need >10 to get to level 4, so you're basically stuck with a level 3 city.
A level 3 fortress with zero essences is useless to me, you miss the city enchantements for unit training and the production bonus coming with the lvl4 and lvl5 (a lvl 5 conclave with 4 essences and alchemist lab is usually the highest production city, the one dedicated to expensive building) - what purpose should it have? Pioneer training? On the other hand if it has 2+ essences it can be useful to train backup units.
A lvl 3 town will generate enough gildar only with 3+ essences and the propaganda spell; less than that the city suffers from the lack of the higher level bonuses (you can have some +% modifers but the base value is too low); it can however be used for the faction-wide food bonus provided by the grocer line of buildings (it isn't tied to the level of the city).
A lvl 3 conclave can produce some research but it can shine only with essences because of the herbalist line of buildings; a high material high essence conclave is the best producing city of the game thanks to arcane forge and alchemist lab, no matter the grain.
So my advice is: 0-1 essence, build a town or salt the land; 2+ essences, build a conclave (you will gain an additional essence with the oracle upgrade at lvl 3) or, if you really need it, a backup fortress.