Check out merging chests mods at https://mods.factorio.com/user/Atria mods for a replacement for this mod.
Is it a feature that when picking up chest of 6, 13 ect that they give that item. Is there no way to craft them back into invidual chest?
Yes it is a feature, I'll look into making it an option to select how you want that to happen.
Feature added, settings, mod settings, select option to pickup to individual original chests.