Smart code navigation refers to a set of features in VSCode. And the PIO Unified debugger is more capable on VSCode (see here). I’d suggest sticking to VSCode for all purposes, it’s just better supported out of the box and has more features.
Of course, PIO also supports other IDEs, you can generate project files from the command line for atom|clion|codeblocks|eclipse|emacs|netbeans|qtcreator|sublimetext|vim|visualstudio|vscode.