You’ll want AT do acknowledge that the particular energy system assigned for that day gets accounted for in your future adaptations. Developing those systems can often happen in really specific progressions in the scope of all of your workouts, so by skipping instead of deleting, AT knows how to better account for that missed day (where just deleting un-does that logic).
TLDR: AT needs you to leave it to know you skipped the workout, will help make up for it later.