If you have a threshold speed set for running in your settings, then TP will apply an rTSS calculation. That’s only relevant for flat running though (+/- a few % in incline). If that’s not your thing, then it’s best to remove the threshold speed entry.
The thing to do with the hrTSS is, first, manually cut out the breaks. You can click and drag over sections of the chart and remove pieces as required. Save the changes, and hrTSS should recalculate it.
If it still feels like an over-estimate, just manually change the TSS to what you think reflects your fatigue after the effort.