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Hi Esad,
In general the two methods should yield approximately similar results but they can sometimes differ, usually by only a few percent. The reason for this is because the direct+indirect report is calculated by allocating demand side consumption back to the various Transformation modules and then looking at their energy use and emissions. But some energy systems have certain features that cannot be fully accounted for by this kind of calculation. The most likely discrepancies are due to imports into a system that typically will have no emissions in the direct calculations (because they are beyond the area boundary) but are intentionally assumed to cause emissions in the direct+indirect calculation. More complex Transformation systems with feedstock flows and auxiliary fuel use can also cause discrepancies.
Hope this helps!
Charlie