Sometimes. Primitive active and passive devices are generally multi-layer pcells (parameterized cells) with variables for various parameters and dimensions to keep them drc clean and assure model accuracy. These are the primitive devices used in custom circuits. We do flatten devices and modify polygons when desired.
Perhaps we have a different definition of standard cell in mind. I think of them as circuits like logic gates, not a single transistor or resistor. The pcells are primitive design kit devices that come from the foundry. Standard cells are libraries of common circuits that may come from the foundry or other IP vendor or have been developed in house. Am I confused?