So, to try and put it as clearly as possible:

I am making a player house mod. In the interior I am placing sacks for storage. I place two MiscSack02LargeFlat_NoRespawn down. I want one of them to contain five sacks of flour, and the other to contain something else. However, when I (through the CK) put flour in one of them, it mirrors to the other as well. I realize that this has to do with that it automatically mirrors the contents to all containers of the same name ID.

My question is, how do I make a container with custom loot? Do I have to make a duplicate object or is there another workaround?

Yes, if you want a container with a specific content, you'll need to create a new form. However, you can create a LeveledList for "random" content and let the game pick from that. If you have two containers using the same list in the same cell, it normally won't pick the same for both.

If you change a form, you're doing that for all the instances that derive from it, so it's generally a bad idea to do that. Duplicate and change the copy only, even for the first one.