e.g. its "run" gutter icons rely on context free grammar queries, but of course Scala allows to define main methods via inheritance from a class. Zed's extension api should let the extension report entry points via whatever internal mechanism it needs.
This also goes for the various testing libraries in Scala that because only tree-sitter queries are supported therefore need a custom pattern match for each library as they have their own mechanisms, rather than letting the extension provide its own test harness (easily handled by build tools automatically) - Zed should provide something similar to VS Code's Test Explorer and Testing API interface.
Also extensions can't add new UI, so you are stuck fitting to the recipe Zed team provides for you to plug into, and often enough this is not satisfactory.