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From what you describe, the short answer is that your Twist message is probably applied in the "'instantaneous' body frame" as you put it, but as @gvdhoorn mentioned, it's really up to the consumer to choose/assume the reference since there is no inherent frame in a simple Twist message. Velocities for a robot are commonly expressed in the base_link frame, which is rigidly attached to the robot base, but it would be equally valid--and sometimes desirable--to express them in another frame.

If it's a TwistStamped message instead, it has a header component, which includes a timestamp and a frame of reference. Then, the answer is more concrete since the supplied velocities are explicitly attached to a specific frame at a specific time. If you want someone to comment on what's happening in your case for certain, please provide more context.