I guess it'll depend on your colour coat, how much you have to rout out, and your personal preference. I prefer to make alterations/adjustments as early in the process as I can, that way I have more options if something goes wrong. And, if something does go awry, it's probably going to be a lot easier to fix a colour coat than a clear coat over colour (depending on what you used). Something like a low tack masking tape may be enough to protect the colour perhaps? I've also found cork-backed placemats can be useful to protect a surface while routing. Maybe you could just pare out the rout a bit with a sharp chisel rather than having to use a router again? But, if you have a fragile/complicated colour coat and you're confident about routing once the hard clear is on then that may be the better option.