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You reference "zone loads (in HVAC Sizing Report)", so the load comparison in this case is from the zone sizing calculation, not the full simulation. If you look at output variables for the HVAC system loads from the full simulation, you should see the expected trends.
Unconditioned, or semi-conditioned spaces must be treated carefully for sizing. If the mechanical room is unconditioned and you use a ZoneVentilation object to ventilate the mechanical room, then the sizing calculation should see a change in the mechanical room temperature and should result in a change in the design load for the zone(s) in contact with it.
But if you are using an HVAC system to ventilate the mechanical room, the sizing calculation knows nothing about this (because HVAC systems are not simulated during the sizing calculations). And if there is an HVAC system connected the mechanical room, then there is likely a thermostat in the model for the mechanical room (even thought it's not really controlling anything). The sizing calculations will use the mechanical room thermostat setpoint (because they assume there's a system available to meet that). So for this case, you're kind of stuck approximating what you think the design temperature will be in the mechanical room and using that as the thermostat setpoint.