Web2Cit-Core should follow redirect statements in configuration files (T304772). This would be used to define domain aliases (e.g. www.example.com = example.com).
However, if one forgets to define such aliases explicitly, Web2Cit would fallback to using Citoid (see also T302019).
Additionally, consider providing an option to make a HEAD request beforehand to the target webpage and using the domain indicated in any redirect responses, instead of using the domain of the original URL.