In real life we all "spread our things all over the house" to keep
them in order.


Exactly. And the point of spreading files all over the directory
tree (not filesystem) is to be able to easily:

- split the tree into several filesystems that have different properties
  such as size, speed, availability when the network is up, etc.
- make part of the tree read only (to protect it from some problems)
- make part of the tree shared between computers
  - and some parts shared between computers of different cpu architectures

For example it should be possible to make /usr read only and
share /usr/share between different cpu architectures.

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