The difference between a re-manufactured and a rebuilt transmission is that a re-manufactured transmission has been restored to almost new condition while a rebuilt transmission has only had the most worn or damaged parts replaced. A re-manufactured part also typically has to meet the original equipment manufacturer standards.
In a re-manufactured transmission, any part that can be worn down is usually replaced with either a new or re-qualified part. The engine core is inspected and only used if it is in excellent condition.
In a rebuilt transmission, replacement parts for worn or damaged components are used parts taken from another vehicle, sometimes from a junkyard. The parts used must be within the manufacturer's wear limits. The quality of the part varies based on the original vehicle.
A rebuilt transmission usually costs less than a re-manufactured transmission. However, the warranty on a rebuilt transmission tends to be shorter and more limited than the warranty on a re-manufactured transmission. Also, a rebuilt transmission, due to the replacement parts used, has components that vary in terms of wear. The transmission could also have wear that cannot be seen by the mechanic, in which case worn components on the rebuilt transmission may not be replaced.