PDF Studio Overlay Comparison Feature allows to customize the colors of the 2 documents that are being compared.
The default red and green colors will work well when comparing standard PDF documents.
For some documents and at lower zoom level, due to artifacts in image conversion or in anti-alias rendering, the compared PDF output might appear yellowish.
Green (0, 255, 0) / Red (0, 255, 0)
Thin lines in architectural drawings might appear yellowish when using pure red and pure green.
You can try using colors that add up to white… which in this case might produce a more neutral output, though not as contrasted. See below for sample color pairs that might work well. The number in parenthesis represent the color in RGB values.
Cyan (51, 204, 204) / Dark Red (204, 51, 51)
Green (0, 204, 51) / Dark Pink (255, 51, 204)
Blue (0, 125, 255) / Orange (0, 125, 255)