I think you are right about the background.
I had another Idea (I can add on github if you like it).
On the plugin page you could add a input box that would allow the end user to use there own switches. This would allow them/me to play with the libwebp/cwebp settings.
I appreciate this might no be the easiest to do do, input validation, unexpected output... but worth a look. 😀
Perhaps also the input box would remember what you had in it on the last run and maybe a reset back to plugin default (this would also be useful to see what the current defaults that are used are).