Getting Stripe Webhooks working
If the Stripe webhook wizard is creating webhooks with the wrong API version, that's a bug, and should be reported on https://lab.civicrm.org/extensions/stripe/issues.

To allay your concerns - it's very unlikely that you're going to experience any ill effects from this.  The check in question is mostly concerned with folks running older versions of the Stripe API, and the API doesn't change that drastically from version to version.