The main reason to keep the air box rather than junk it is it gives the engine a certain volume of still air to feed off. With the air box removed that still air supply is removed.

This is how the air box mod came around. As stock the 2 stock intakes restrict the inlet, once these have been enlarged by way of either the tyga mod or the 4 holes you have the benifit of a unrestricted lid and the volume of the air box for still air.

HRC never ran the carbs fully and always used the HRC air box Andy makes. This lets the carbs run open so they are in no way restricted but also provides still air for them to draw off.
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If I have to take the carbs off once more...