I don't do it meticulously or anything but I do sort elements into their similar parts (ferrite, pure ferrite and magnetized ferrite should all be together). Mostly just stick colors together. Then move things I won't use very often towards the bottom or stuff them in slots that are secluded (before I have my full inventory unlocked).
Genuine question here as I'm still new to the fediverse.. isn't defederation a one way street? Like if an instance defederates from Threads, they can no longer see anything from Threads. But Threads can still see things on all the instances? If that's the case, it doesn't feel like it's hurting Meta too much if other instances defederate from it.