The most reliable workaround I have found is using the CMAKE_EXPORT_COMPILE_COMMANDS option. With this (but only when CppTools extension is installed), one can type IntelliSense in the Command Pallete, which offers the option to choose the data source. And then one can select the relevant compile_commands.json file. Once this is set, the navigation through Ctrl-Click seems to work correctly within the source which belong to the selected build target.