It's not totally clear on the OTR website - they kind of imply that if you fit the side cover (with no other changes) this equates to Stage 2 (which it may well be equivalent to), but that isn't what a Stage 2 set up actually is. Here's a rough guide (in pictures) that's hopefully a bit clearer:

= Stage 1

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= Stage 2

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= Stage 3
Removing the snorkel effectively does the same job as fitting the Stage 2 DNA airbox top.
There is also a restrictor insert you can fit in the Stage 2 top cover to effectively make a Stage 1.5, which would be as far as you could go with out modifying the fuelling to suit.