TL;DR: In your bricklink wish list, select all parts (the uppermost checkbox), and select Apply: Color, and choose "(not applicable)" and all your parts would be shown with the most common color. (and you could buy them with no problems)
Using the ignore colors option, wil get you into 2 little bugs:
The missing part list, shows all parts with "color error" and in blue color. I'ts not very critical, since you still get a clear picture of what parts are you missing, but displaying these parts with the set color / most common color would be ideal.
If you export that list, the color problem still persists, the exported document has all parts with the color ID set to 123 (or -1 depending of the export format). At least for bricklink you could get arround this by opening the file with a text editor and replacing "<COLOR>123</COLOR>" with noting. Your list will import just fine and you could shop your whislist with no problems.