It will basically restrict discovery of references to the main source file only. E.g. if you have a template function inside the main file, but it’s instantiated somewhere in a header file, that instantiation will be ignored and the function body won’t be colored properly (that only affects template functions and only if they are not used inside the main file itself).
It might also interfere with the ‘find all references’ functionality for translation unit-scoped entities (e.g. static functions), that are declared inside the main file, but used from headers (this won’t affect finding references for regular functions/classes, as it involves scanning the entire project using a different mechanism that is not affected by this setting).