The Reference Point is always the beginning state of the system.
The Second Law applies to systems in isolation, it could be applied to the Universe. Entropy increasing means "less energy available" for work, work is required to create order. This means all systems, however ordered in the beginning, tend towards a homogenous state where entropy is maximized. In such a state, no energy is available for work, hence, no order. Do not confuse a homogenous energy background for order, it is chaos.
You have that 100% backwards Emile. This physics, not religion, though they may be related.
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