How did you create a draft from a content is not published? Using the API? Cause I'm not able to do that using the editor interface.

However my impression is that Primary Draft mainly refers to "what version do you want to start to see when you're editing" and would have nothing to do with master language properties while this code gets the work done for me. Did you do something similar?

var contentRepository = ServiceLocator.Current.GetInstance<IContentRepository>();
var page = contentRepository.Get<PageData>(new ContentReference(12));
var clone = page.CreateWritableClone();
contentRepository.Save(clone, SaveAction.Save | SaveAction.ForceNewVersion, AccessLevel.NoAccess);

Normally it always use the published version on the Master Language for non-culture specific properties but It looks to me as it's picking the first created version as there are no published ones. Which might explain why you can't remove that first created draft on the Master Language (at least not using the editor interface).

I don't think it's that common that there are multiple drafts of a page (or have I missed something?) or that editors start working on their translations until the master language is published so might not be a behavior considered by Episerver.