Hello,
The best way to use markers/control points to create a reconstruction region is to set the reconstruction region on control points. You can use that manually in RealityCapture in the Set Reconstruction Region dropdown, or through batch file (command line).
If you are doing it manually, use this tool and click on three control points and height of the reconstruction region can be set to anywhere. You can change it later in MESH MODEL tab / Info panel to a certain value.
If you want to use command line, there is a command: setReconstructionRegionOnCPs. Contact me on support@capturingreality.com and I will send you a CLI sample to see how to do it.