The very first and perhaps the most important difference between the indexed results of site operator and Sitemap is:
“Your Sitemap report provides more granular statistics about the URLs you submitted, such as the number of indexed URLs vs. the number submitted for crawling, and Sitemap-specific warnings or errors that may have occurred when Google tried to access your URLs.”
Site operator results can show you:
- a rough estimate of how many pages have been indexed
- one indication of if your site has been hacked
- if you have duplicate titles or snippets
The Sitemap report just reflects the URLs submitted in the Sitemap file but on the other hand, Site operator takes into consideration whatever has been crawled by Google, as explained by Search Quality Team, Google
For more information, check out the Help Center for Site Operator and Site Map
