Hello,
when importing E57 from RTC360, the registration is preserved, as you correctly mentioned.
After you import pics and follow the Agisoft document you mentioned, then it happens that laser scans are unlocked and the combined pointcloud + pics is georeferenced with positions from pics, so registration of laser scans is lost.
There is workaround (a python file that could be requested) from Agisoft allowing, using GCPs, to register laser-scans again, but it is not state-of-art solution and we hope that a new method will be implemented in next versions.
For what i know, there is only 1 software that operates combined photogrammetry with laser scans that is 3Dflow Zephyr, but it is really really slow and results are not so enthusiastic: I am pretty much sure that once MS will implement this new features, it will be top peformance solution as usual!