If I'm understanding correctly, this isn't a bug, but simply how persistent variables work in Ren'Py. When the default of a persistent variable has been set once, updating it won't change anything. I might add a note within the plugin to make this clearer in the future!
Using Delete Persistent from the launcher should let your changes to the default value take effect. (Though keep in mind this might also reset some other settings for you.)
Otherwise, if you don't plan on using the preferences menu / having the player be able to change the values themselves, you can swap default for define (for example define persistent.speech_pause_comma = 0.15) and this will make the game always override it with the values you set!