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Most output reports are documented in detail in the Output Details and Examples document, but I see that this documentation hasn't kept pace with some of the reporting changes over time, this report included.

In general, for reporting of sizing results, "Design" values are calculated by EnergyPlus sizing, and "User-Specified" values are directly specified (e.g. hard value for a flow rate) or modified by a user input (e.g. multiplied by a sizing factor). The user inputs that impact "user-specified" values include sizing factors and flow rates in the sizing inputs (ref. Sizing:Parameters,Sizing:Zone, and Sizing:System) and hard values in the component objects.

Which values to use? Often, there will only be a "design" value reported, so that's the one to use. If both values are reported, then the "user-specified" value should be the one to use assuming that all of the inputs are correct. When the two values differ significantly, it is important to understand exactly why based on the detailed inputs in the input file.