The mod wasn't creating a stacker variant for modded loaders, in this specific case, TurboBelt's green SA-equivalent loaders.

TurboBelt uses AAI Loaders native function to create its loader, but because TurboBelt loads after this mod, this mod does not create a stacking variant for that loader. Adding TurboBelt as an optional dependency fixed the issue and created the stacker variant correctly. Of course this isn't an automatic fix for any mod that uses AAI Loaders function to generate loaders, but maybe there's a way to force your mod to generate the stacker variants last, after all other mods are loaded.