At the geometry level, 3MF represents triangle meshes plus multiple objects, units and print metadata. PLY represents vertices, faces and extensible per-element properties. A flattened surface can be dependable when the receiver only needs final triangles, but it is a destructive handoff when someone still needs editable solids, object hierarchy, animation, vertex attributes or manufacturing metadata. Once those semantics are discarded, converting the file back does not reconstruct the original design intent.
A safer production workflow keeps the richest editable source as the master and creates a separate delivery copy for a named destination. After export, inspect units, bounding-box dimensions, up axis, normals, watertightness, object count and material references in the receiving application. The main 3MF caution is that it support is newer and less universal than STL or OBJ. The main PLY caution is that it scene structure, animation and broad consumer-tool support are limited. These are workflow constraints, not minor technical trivia.
The practical verdict is to choose 3MF when the job centers on modern 3D-print handoff between capable slicers and print services, and choose PLY when it centers on 3D scans, research datasets and colored point or mesh capture. For 3D printing, the slicer's actual import is the final authority. Confirm millimeter dimensions, orientation and mesh integrity before generating toolpaths, even when the preview initially looks correct.