The beauty of the reconciling assistant is that it makes things easy by importing from your bank file. However, you're right, it doesn't always match what actually happened in terms of when things happened due to some banks not posting things on weekends. Most people opt for using the bank file as truth simply because that's what matters to the bottom line. Other reconcile once or twice a week and move the items as needed using the “Mark as completed” (found by right clicking on an entry) to indicate that this item now matches the bank statement and is locked in. Others only do it manually.
Its a choice you'll need to make. I find myself in the middle group using Mark as completed and reconciling regularly.