Fix two issues of user key map for extension commands.

This fixes #9954 and #9953.
Do we want to introduce the `userBindings` parameter to the `addBinding()` public API? Seems like manipulating the user key map should be done internally so new parameter is only necessary on `_addBinding()`.

This can be fixed by changing the calls to `addBinding()` in this file to use private `_addBinding()` function. It seems like unnecessary processing to use `addBinding()` in these cases anyway.