When working in a packaged file workflow, where Adobe Fonts are not and cannot used, if there is a missing font that a user might already have enabled in Adobe Fonts, InDesign makes a font replacement with no warning.

There is an alert to activate missing fonts, but no warning if missing fonts are already activated in the user's system. I’m not sure if you could limit this to: If there is a Document fonts folder present, then there should be an alert before fonts are replaced with Adobe Font versions. This should not effect if fonts are enabled in other font managers.

For example, if Scala Sans Bold (OTF) is missing from the Document fonts folder for a file, and the user happens to have Scala Sans Pro Bold enabled in Adobe Fonts before opening the file, InDesign just makes the replacement without warning. The user sees no missing fonts, packages the file, sends it to someone else without this font enabled, and the font is missing. This makes it difficult to maintain a strict package workflow.

This is critical for licensing when files may be worked on by outside vendors or freelancer not working solely in packaging workflows, where access to Adobe Fonts is not controlled.