I don't know how you are using it so it hard to give a definite answer but...
Chipboard is preferred as MDF is very sensitive to water. if it gets wet it will blow apart, whereas the resin in chipboard (or OSB oriented strand board) makes it better at resisting water.
Ideally if the water proof covering is fitted properly water should never come into contact with the board. However, if it does you will be glad that the chipboard is there, as you will be able to find and fix the leak, without tearing up your whole roof.
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