PKHeX is open source, you can see its conversion routines.
Overriding your settings to No will skip updating things to match the save file. Eggs from other trainers must be traded, so they must be updated to be met as a link trade egg instead of from daycare. Handler states and memories must be adjusted as if a new (or previous) trainer is handling it. When no, it skips doing all that, which lets you inspect the original values. Again, you shouldn't need to override it.