site:example.com is the first thing every SEO learned — and the most misread signal in index checking. Short version: useful flag, terrible verdict.
Google's documentation describes the site: operator as a way to restrict search results to a domain or prefix — and states outright that it doesn't necessarily return all the URLs indexed under that prefix. It is a filter over what Google chooses to serve, not a database query over the index.
Quick spot checks, sanity-checking a section's presence, and estimating (roughly) how much of a competitor's site is visible. For anything with consequences — client reports, vendor disputes, migration sign-offs — verify with multiple methods: for one URL, quoted search plus URL Inspection; for a list, a bulk index status check that cross-verifies each URL with several query types (site:, inurl:, direct URL, quoted match) and marks a page “not indexed” only when they agree.