I have two sets of color filters that I wouldn't use under the negative.
The better set is marked "Unicolor," and there aren't obvious image destroying qualities in that set other than scratches. The other set is only marked with the color values. This cheaper set, when viewed at an angle, reveals sort of a striped pattern like stretch marks in the base material. I wouldn't use either set in the D2.
My multigrade filters, are hard plastic and clean and obviously designed to be used under the lens. So that's where I use them.
But whenever I need longer enlarging time, I toss a two-stop No. 96 ND filter on top of the lens.