Adjust recipe due to plate chiller liquid lost?

Brewed a schwarzbier last week and noticed at the end of the boil that we had between 5.25-5.5 gallons of wort.

Pumped through the plate chiller and when the boil kettle was empty we noticed the carboy was only full to 4.75+ gallons. This is a 30-plate chiller

Do you all adjust your recipes to have more post boil wort to accomodate the loss inside the wort chiller? or do you force extra wort out of the chiller?

When cleaning our equipment and pumping sanitizer through we counted around 2 quarts of wort trapped inside the plate chiller.

Yes, software should account for wort loss in trub and chiller. If you can keep a siphon going, it should clear out though.

Yes you should account for all your waste. Measure how much you typically leave in the kettle, chiller, hoses, etc and account for it when you do your recipe. Also consider any transfers you plan to make and how much you plan to leave each time.