If you call someone big-boned, you are saying they are large because their frame is large — wide shoulders, thick wrists, a heavy build — not because they are simply carrying extra fat. Families often use it kindly: she is not fat; she is big-boned. That is the tidy story. Though actually, people also use it as a soft, polite, or even joking way to avoid the word fat, and listeners often hear that second meaning. So it can be sincere — some people really do have a larger skeleton — or it can be a gentle cover. It is informal, and it is about bodies, so it can sting if you use it about someone who did not ask.