Can someone explain the logic behind the natural ordering of the Instruments?

For example, take

this.context.getSubscribedInstruments().toArray();

This will return an array of instruments (as Objects).

If you then do Arrays.sort() on the array, it sorts based on natural ordering. Natural ordering is implemented via compareTo() from the interface Comparable.

The ordering isn't alphabetical. It doesn't order based on the primary instrument vs secondary instrument.

For example, AUD/JPY, AUD/NZD, AUD/USD come first... then lots of others, then after USD/JPY once again we get AUD/CAD and AUD/CHF.

What is the order based on?

It is made up from sequentially added chunks of currency pairs, i.e. new instruments get added at the end of the instrument list, instead of inserting them in the middle of it just for the sake of alphabetical ordering.