Is drilling into the MDF wasteboard ok?

I’ve had 2 snapmakers 250s and I’ve noticed that the bed is not level causing issues with milling things. After reading some posts here, it seems that people just mill a piece of MDF to make it flat as one way of compensating for it and placing it on top of the wasteboard. I’m not sure how that would work since that would cover the screw holes on the wasteboard.

But I realised that I could just mill it deeper and go straight into the wasteboard in order to fully cut my parts out. The question I have is, is this normal for other CNC machines? Is the point of the wasteboard to just drill holes into it? I’ve been trying to avoid damaging the wasteboard much because I do like the markings on it as they help me align materials for repeated jobs. It also feels like I’d need to replace it at some point if I keep doing that since it’ll be uneven.

Even though it’s called a wasteboard, or spoilboard, you may consider using another layer attached to it as the sacrificial layer

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