I would consider the carbon wheelset of the Canyon a pretty big benefit over the aluminum stock set on the Santa Cruz, with the big caveat that I have not ridden either. Santa Cruz’s carbon wheels are well respected, but I suspect it would be a decent jump in cost for them, but worth checking into.
@stringwise makes a fantastic point about spending a little more to get a higher spec. It’s almost always cheaper to do that at the time of purchase rather than paying for more upgrades later.