The difference is in the fidelity. A flight sim models a particular a/c type & model. Inside it looks like and, to different levels of success, feels like the real thing. Motion & visuals are a requirement,
AFAIK. As an approved flight sim the time can count towards a type rating, type recency etc
An FNPT device (JAR speak) or equivalent doesn't necessarily have to model any particular a/c. It might on the surface look like a King Air or Seneca however it need only fly like a generic aircraft. Motion is not required but may be present. Visuals may be a requirement depending on the class of FNPT approval. FNPT experience generally only counts to meet some of the IF time needed for an IR or whatever.