My mistake about the help file! I think what I said only applies to the Bitmap Font plugin, not this one.
I *think* that this window and scene font command is how it is supposed to work. This means the Window/Scene must be closed/open for it to work, so they will be refreshed and apply the changes.
But, the Yanfly overwritting or not, depends on the plugin order. If my plugin is below yanfly ones, then they will not be overwritten.
I don't know if I will take a look into this. But if I do, I will tell you here.