Which specific key(s) did you have in mind ?
The text you quote means to say that you can't use this methods when there is a property in a configuration spec that controls the value of a specific VMX file entry.
The VMX entries that are configurable (add & edit) this way, can be set through the reconfigVM_Task method and the extraConfig property.
See for example Steve Jin's post called How to Change VMX Programmatically?
There are several examples in this community as well.