I suggest that the default PackageHelper::getSiteListForSiteModule could be replaced by a extension configuration.

Reason

EXT:bolt requires extensions to have the prefix site_. In a current project, we use the concept of "layout" packages, that renders content. They are prefixed with a different prefix than site_.

Suggested solution

I have a POC at hand for this idea.

Via ext_conf_template.txt the strategy can be changed to a different class, implementing a single method, returning a collection of site packages that can be selected in the backend.