Isn’t the original situation the behaviour of a proper separation? If the characters in the equations are black, they will knock out any background colour by default; turning off the Black will show that knockout (the absence of any colours) as white in the shape of the characters, which is technically different than white text on a colour background. If you overprint, then the background colour will be untouched and added to the Black, turning it into a rich black, and the equations will definitely be darker than any surrounding black text. I don’t think anything needs to be done to those equations.