QL is internal ballistic software that is just like external ballistic software in one regard: NEVER LIE TO IT
Enter all values correctly, and tweak only the CAUSE of discrepancy.
For example, a fast/slow lot of powder may need a Ba adjustment, but different seating does not change anything about the powder. So don't adjust Ba for seating changes. If you do that and save the powder file, then you have created no more than a bogus powder file.
And when you do a Ba tweak, you should also test that powder in another cartridge. If your new Ba is correct, it will not need further adjustment in another cartridge. Then save the custom powder file for credible use.
For a load-pressure curve needing expansion/collapse, use 'weighting factor'.
Make sure your bullet's shank seating depth is correct (don't use COAL), and your barrel length is correct, and H20 capacity, and if you end up with a ~50fps discrepancy then run it with different QL barrels. YOUR barrel could be a faster/slower barrel with a different cross-sectional bore area. QL was kind enough to provide plenty of bogus barrels (and powders) in their system.. Test barrels & powders from different realms I guess.