I kind of doubt filing or in any way modifying the shape or edges of the upper/higher vacuum platen area is really going to fix this issue for you. It is the areas lacking support where the vacuum builds up and pulls the paper down into that area that is really the culprit. Think vacuum forming of hot soft plastics, in this case wet limp paper.
I can think of two possible options, depending on your level of commitment to using the 9880 for what you are doing. The first is pretty quick and easy to accomplish, the second might take a good bit of fiddling to get accomplished but might be a better long term fix.
One, take a strip of packing tape and lay over the vacuum platen area, and then punch all the small holes in that, such that there is more support for the paper, instead of the bigger/wider gaps, that allows the dampened softened paper to pull down into the trenches and how it gets deformed. This option might cause initial paper feed issues if the top edge of the tape catchers the leading edge of the paper, or others?
Two, find some really firm open cell plastic and make form fitting plugs that press fit in the depressions of the vacuum platen area, so the paper doesn’t get pulled down in the open trenches, i.e. vacuum formed.
That is what ultimately going on here, vacuum forming of the softened paper.
Later Larry