The standard Checkpoints report pulls through the "estimate of ability" target for the end of year, so you need to make sure that you have the same options selected when running the Simple Tracker report.
By default, the report selects the estimate of ability target for the end of the key stage. To match the Checkpoints report, set the toggles to the following:
- Toggle Targets: Estimated
- Toggle Stage Targets: End of Year
- Toggle Names: Student Name (of ID if preferred)
Your targets should now tally with the main Checkpoints report.