Bed "Flatness"

[EddyCurrent]

If you are cutting right through the MDF and you don't mind going slightly into your ply spoil board then I don't see why you should skim it. The only thing that might occur is that if the MDF is sloping badly then any vertical cuts would not be at right angles to the MDF surface and that may or may not have consequences for your application e.g. parts not fitting together correctly.
If you intend to make cuts that do not go right through the MDF then the ply would need skimming, probably using the biggest diameter tool you have.
Be aware that if the spoil board extends beyond the footprint of your tool travel you would effectively create a pocket in the ply and your MDF would need to fit inside that pocket to be flat.