Be smart about rearranging your cargo and things should be fine.
The further along you get into Death Stranding, the more cargo of varying shapes and sizes you put into Sam's handy auto-expanding backpack. This can start to look ridiculous after a while, especially if you're stacking deliverables and gear on your back with no rhyme or reason. In the world, you can only really grab cargo and put it in your backpack, but if you pause the game and go to the Manage Cargo screen, you can be more granular about how you organize your stuff.
Thankfully, the process of transferring stuff across your backpack and various pouches is made easier thanks to the Auto-Arrange Cargo option, which allows you to optimize everything in your possession automatically. While this is the go-to way to ensure you're always carrying cargo efficiently, it doesn't always optimize for special circumstances.
Be mindful of factors like special cargo, such as pizza and cryptobiotes, which both call for being packed in particular ways; pizza needs to be positioned horizontally to avoid being ruined, and crytobiotes need to be packed higher up in your backpack to avoid contact with water. The Auto-Arrange option will typically pack this cargo deeper into your backpack instead of placing them where they can be kept from harm.
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Auto-Arrange Cargo also doesn't take into consideration what's most efficient when it comes to what to equip onto your tool rack. For example, if you have a Bola Gun--which takes up two small cases worth of space in your bag--Auto-Arrange will often place it on your back instead of your tool rack. A simple reorganization will fix this, but it's something to consider whenever you're dealing with tons of large, heavy cargo and are looking to save on space.
These two examples are small, yet significant ways that the Auto-Arrange Cargo option can negatively impact you. Keep them into consideration, and you should get along fine using Auto-Arrange to optimize your loadout. For more Death Stranding features, check out our in-depth beginner's guide and our gallery highlighting all the most significant celebrity cameos we've found so far.