Would depend very much on tyring and gearing.
My CX wears 28×700 GP4’s for commute and town duties. If I’m not really feeling it I average around 20-21mph and peak out at just over 30 in the same places every day. It’s around 6 miles and a not-really-going-for-it day is around 18mins. It turns in much the same times and averages with slightly lower peak speeds with the 32×700 Crosswolfs on it but is more effort. I did the Way Of The Roses on the Crosswolfs and it wasn’t too slow.
I’ve ridden 26er MTB’s and fat bikes on the same route and eventually (after a week or two) get to around the same times as a slow day on the CX but again without the peaks, but with much more effort. I generally prefer the CX for this as I like the sprints and it’s been deliberately setup for being around town vs my MTB’s which really haven’t.
The CX with either tyre setup I can be faster for longer is all, really.
I’ve not put it up against a 29er, might be interesting to see. I suspect it will be the same though, as effective gearing between a 26×4 fat bike and a 29er are pretty much the same, just with more traction and inertia on the fatty.