In your use-case, when trying to fix non-identified pauses, it's right that trimming is not the right thing to do.
Still, the warning message remains valid. There are numerous calculations based on the recorded data and not based on the average/total values. Simply adjusting the total duration will not correct those calculated values and there's no way to do so.
If your watch does not support auto-pause but you want to exclude pauses, you should stop your watch manually.
So far, there's no auto-pause detection feature in Runalyze even if it's on our long todo list.
