when C3 is generating spritesheets, it seems like memory usage skyrockets the more images there are, and very often it leads to memory overloads.
I had assumed the previous discussion related to the runtime. If you are talking about the editor, that is quite a different matter - it may cause you some problems during development but it should not affect the experience of gamers playing published games at all.
FWIW the editor has a fixed limit on how many spritesheets it will render at once, specifically to cap the memory usage. For example if you have 1000 spritesheets, it will only render/compress something like 10-20 (I forget the exact limit) simultaneously at any one time, so the peak memory usage should only ever be the amount of memory used by the handful of spritesheets that are currently being processed.