Present perfect talks about a time period that starts in the past and continues into the present. In the following sentence, however, the time frame doesn't continue into the present, the moment of speaking. Why can the present perfect work?
Every day, by the time we get home from school, mom has prepared the dinner.
The sentence you’re referencing here would be better rewritten as:
Every day, mom prepares dinner by the time we get home from school.
Your current sentence is rather ambiguous in timeframe. It works, but isn’t ideal. And to answer your question more directly, the timeframe actually does continue into the present, the moment of speaking. You are saying that mom regularly prepares dinner by a certain time, an action that is continuing to the present. That is what the “every day” indicates: that this action is ongoing.
“By the time” merely indicates a more specific setting for the action in question. For example, in this sentence:
Every summer, when we go to my grandparent’s house, we swim in the lake.
Here, “when we go” would serve a similar purpose to “by the time.”
Finally, “has prepared” serves to further specify the details of the action. It tells you exactly what the action is. You could have said, “mom starts preparing dinner” and that would have been fine; it would mean that the action here is “starting dinner.” So here, “has prepared” doesn’t indicate that mom finished cooking and is no longer cooking in the present. It only indicates that, on a regular/continuing basis, mom finishes cooking by a specific time.
