Recap registration should as default only rotate scans around z-axis, not x- and y- axes.
Recap registration assumes the first (or chosen) scan is level and aligns all other scans to the first one, tilting the scans around the x and y axes for best fit.
It discards any levelling information of the remaining scans.
This works well for a handful of scans but it leads to big problems, if there are more than a few scans between the first and the outermost scan. Floors that are known to be level appear as curved or wavy over larger distances in the registered point cloud.
In other words, the elevation measured from the point cloud cannot be trusted.
The workaround is to measure control points with a total station.
There is also a cheating workaround: create fake control points on the floor and set z=constant.
Scanners generally measure the inclination quite accurately. That's why the scans should by default not be tilted during registration. Other registration software I know work just like that: by default scans are not tilted, but the user can unlock 3-axis rotation on a scan-by-scan basis to handle problematic scans.