This is the expected behavior. RT structure set is very poor 3D representation, as it is highly anisotropic (contains high-resolution contours within a slice, and there is no information about contour shape between two slices).
Segment Editor module performs all editing in 3D labelmap at the chosen resolution. If you find that the default resolution is not sufficient to represent all relevant details then use higher resolution. A simple way of achieving that is by creating the binary labelmap representation using an “oversampling factor” larger than 1.0 (e.g., 1.5-2.0).
Instead of just changing oversampling factor, you can specify custom resolution and extents using “Specify geometry” button in Segment Editor module.