Yeah that’s where I am almost positive it won’t help. Last time I looked at it you can probe as many places as you want, it will average those points to a plane. It does not compensate for a bump or dip. It is meant for a glass or metal bed not being mounted correctly not an uneven surface.
I think you have a good idea though just punch some holes and throw a shop vac on there, I’m sure it would make a big difference.