How to Make Colorful Qr Code for Data Merging?

All showing, once again, that while InDesign's QR code generator is a good start on the feature, it really needs a round or two of expansion and TLC to be a fully useful, flexible asset.

A QR code is just a graphic once generated. You can color it any way you like in any suitable tool, as long as you preserve good contrast and completely color each pixel. (You could probably mix colors across pixels, but it would likely degrade readability.)

ID'S generator will allow almost any base color, but I believe there's a limitation on color spec from scripting and data merge. But once created, you can color away.