Surveyors often use custom coordinate systems or at least a scaling factor to adjust from grid to ground. We recently purchased the DJI M3E with the D-RTK base. I thought orientating with ground control point and selecting local would take care of this, but getting large vertical errors in validation points. Has anyone else found a solution to this?

I typically go to a project before the surveyors and layout the GCPs where I want them and fly the project. The Surveyor then comes and shoots GCPs and his property corners at the same time. What is the best workflow for RTK drones like the DJI M3E?

Not sure if this helps but, I use the Phantom 4 RTK and use a similar workflow.  I either shoot my GCPs in an arbitrary local coordinate system with a robotic total station or have a surveyor shoot them in as local coordinates or modified State Plane (which is still basically local coordinates).  When a survey point with a real elevation is nearby to pull off elevation, I'll tie into that for Z.  To make sure the job processes correctly when Orientating, I always bring in the GCP file as "Local Coordinates".  This approach has worked well for me I usually have very little vertical error.