It looks like you’ve correctly identified that you can programmatically set the Webhook Endpoint API version.

As to why Stripe is indicating that your default version is 2020-03-02, there is an account-wide default API version that is separate from the fixed API version being used by your SDK and can be upgraded from the Workbench. This account level default is used to determine the default API version used with raw calls and was previously used to set the default API version used by loosely typed language SDKs. Newer SDKs now default to the most recent version at the time of release but the account level default is still required for backward compatibility.