Updater code has concept URI hardcoded as starting with http://. This means that if Wikibase instance has https:// concept URIs, Updater can not process it properly. While concept URI does not have to be same as HTTP URL, there is no reason to not support https:// concept URIs properly.
Note that --wikibaseSchema works for Wikibase access URLs (i.e. URLs used to access actual data on Wikibase) - but those are different URLs from concept URLs in the RDF and could have different schema. So we need some better options here.