The inclusion of unknown incarnations of the Doctor on the main article does look good. I do believe, however, that unknown incarnations such as The Doctor (Battlefield) and The Doctor (The Cabinet of Light) should keep their own seperate articles. The length of their appearances justifies more than a simple mention, as any other established Doctor would have. Just because we don't know the specific incarnation number for that Doctor shouldn't mean that the incarnation gets shelved to the main article. We need to remember with regard to this topic that we treat all media as equal on the wiki, so these unknown Doctors could easily by the Twentieth Doctor, or the Ninety Third for all we know. In this instance the main Doctor article should remain as it is, where these unknown Doctors are mentioned but are linked off to their own articles for more information.
The example of The Doctor (The Giant's Heart) is another case, though, I think. This incarnation could be any Doctor at all, and hasn't been established as apart from any other established Doctor, like The Doctor (Battlefield) is. My opinion on this case is that these "muddy water" incarnation should be left on the main article with no link to another page, perhaps under an "unclear incarnation" heading.