sizes of inventories and similar are part of vanilla factorio and are saved with the map together with the entire state of the game. vanilla functions (eg researches) may change these values, as well as mods like this one. but once the values are changed they are part of the game state and need some action to revert the change. in contrast to new buildings and similar that are part of a mod and that vanish once the mod is disabled, simply disabling or removing the mod that did some such change to system values, only prevents further changes to happen but does not revert existing settings.
to set values back to the values that you want or expect, you need to install a mod that allows to change the values, then set the values to the values you want, and then you can disable that cheat mod again. my first attempt probably would be to use "creative mod" to do that since it is the most complete collection of cheat options, but there may be several other mods that allow to change some values.
you also might be able to edit the source of this mod so that it reverts some changes, but that is probably complicated without any knowledge of programming mods yourself, and since most of these changes are probably made only on map start, chances are not optimal to have success fiddling around with the source yourself.
