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I believe the Heat Rejection heat transfer you are seeing in the first case was reported by the chiller and it represents the heat rejected to the condenser loop by the chiller.
Unfortunately "EnergyTransfer" metering is not really comprehensive, there are so many different heat flows going on inside it gets to be too much to try and report everything.
You can always check the meter definitions ".mtd" file for a description of what is really on each meter and this is more important for heat transfer meters.
In looking at the source code I don't find anyplace where the cooling towers are reporting EnergyTransfer as HeatRejection. They do put all the electricity consumed by the towers on the Heat Rejection end use but the towers don't appear to report the amount of heat transferred. Nor do I find any of the water to air coils reporting this.