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Here are some possible causes for the area not being what you expected.

1. Some spaces may not be assigned to a thermal zone
2. Spaces may be in a zone but not part of the building area
3. Zones might have a multiplier on them
4. Multiple spaces stacked vertically that are part of the same zone may report differently with this script.
5. You may have a space not assigned to building story for story 2 or 3 that should be.

In current versions of OpenStudio there should be warnings if the Area reported in the EnergyPlus report doesn't match the area reported in the OpenStudio report, depending on how you are running the simulation that error may be harder to see.

Incorrect areas will certainly affect EUI since it is normalized by area. Depending on the cause of the difference, it could also impact plug loads that are normalized per area, which would effect overall consumption (even when not normalized per area)

As a note the Space Type Report user script is very old, and probably very basic. It is probably looking at the raw geometry area, and not looking at if a space is in a zone, if the zone has a multiplier, or if zone is included in the building floor area.