Running through the game a second time, skipping many of the side quests, I've noticed a few things I missed my first time around. One of the more major things I've noticed is that the chests made available to me in the Soul Box in route C/D were different. I seem to recall getting more than I got this time. This is reinforced by the fact that there was a voice commending me for various things and telling me I was being rewarded for them.
If there are, indeed, different rewards in the Soul Box, what are they and what are they for?
Best Answer
I managed to find a thread that has amassed a list of rewards and the criteria required for each one based on what the voice commends you for.
It may depend on your playstyle and overall goals, but the most important reward is the Faith weapon, as there are trophies and an ending related to collecting all weapons (not to mention the chips given do not have diamonds and thus, have very high memory costs and could be fused on your own for less). Both times I've gone through this part, I've received the reward for machines killed, so it seems virtually unmissable. If you are attempting to collect all of the weapons, you don't need to worry about not killing enough machine lifeforms.
It's also worth mentioning that even if you miss out on some of the chests the first time you do this in your file, you can always use chapter select to go back to this point. Any chests you didn't have available the first time that you've met the criteria for since will be made available to you if you return to the Soul Box via chapter select.