I believe that there is actually a separate question pertaining to the auto-sizing for multiple chillers which has been buggy in the past, which is separate from the issue of why the values might vary between the two reports in a general sense.

This issue has frequently come up when auto-sizing multiple chillers unless this has been remedied in recent versions of the software. You'll need to go back and enter the capacity for each chiller and re-run the simulation once you've established the loads.

For your design case models, you should have the proposed capacity from the engineers, auto-sizing will only be in the early stages of the project where the capacity may not yet be determined and for the baseline case where there isn't a designed chiller.

As far as the variance between the two reports, verify what method you are using to size the plant equipment either the connected coil capacity or the modeled coil load (which often will be less), and if any oversizing is included.

Autosizing can be problematic for any component in eQUEST, but it appears to be problematic randomly.

I've had to hard enter capacities for chillers, boilers, and preheat coils in the past to get them to work properly.

It's important to look at the hourly reports to confirm set point temperatures are being met for every hour.

If you're early in the design, you can use ASHRAE 90.1 guidance and over size your chiller by 15%, and your boiler by 25% to have a realistic capacity.

Good luck.