After exporting the results, Sum the Amount column from the second query above and notice that the total amount from the excel sum is different than the CRM sum amount from 1 above.
In CRM the SUM action/operator does not take into account the "Suppress duplicate rows" feature, which in this situation is likely added to the second query that is not summing the Application Details\Amount results in CRM.
You can view these settings within the "Set save options" tab while editing the query.
In the second query, make sure this checkbox is unmarked and save the changes, then export the results again.
Both query results when summed in CRM and in the excel file after export should be equal.