With the removal of track as you stated, you would not have to worry with clearance issues.
I worked for CSX for 37 years. Our most vital measurement was top of rail. When building new tracks, we did have top of subgrade for the installation on ballast after that. Over the years with rail change outs, surfacing teams and tie teams the top of rail does change, that is why you measure from it and not subgrade. I always had a height pole with me when doing any track work around overpasses to make sure we were still in tolerance.
Railroad clearances are not always so tight. At times you do have immovable objects that you have to account for. I had one overpass that was close, with only 6 inches to spare. They are replacing the overpass this year to a new height of over 26 feet. The other areas are around industries and tight curves.
