Sadly no, you can't add new rows to your table by doing an external lookup. All the external lookup will do is add fields to existing table rows.
What you can try is a three project approach - assume data sets A and B.
Project 1 - open A, lookup from B, export to C.
Project 2 - open B, lookup from A, export appending to C
Project 3 - open C, filter as required.