Try the workflow
Copy each column without its header, then paste one into A and one into B. If you copy multiple columns at once, select TSV and choose the desired column. Open the tool.
Copy the example
00123 410 550
00123 550 900
Check the result
Only in A shows 410, only in B shows 900, and in both shows 00123 and 550. Keep SKU columns formatted as text before copying to preserve leading zeros.