Can I change configuration values using webextension?

As stated in the question.

No.

As plenty of other posts here would have told you.

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It would help to know what exactly you want to change…

Chrome has support for changing some of the settings, but via special APIs like contentSettings:
https://developer.chrome.com/extensions/contentSettings
There are more, just look at:
https://developer.chrome.com/extensions/api_index

If these APIs are not supported by Firefox yet, maybe create a request on Bugzilla for it?
https://bugzilla.mozilla.org/

Some specific preferences will be exposed to WebExtensions. There’s a tracking bug for them here. There won’t be open access to all preferences, however.