Kyle,
If you set Editor.EditCompleteDocument Property to true, the editor will process content outside the page body and preserve header tags (e.g. <head>...</head>, <title>...</title>, etc.).
All the elements inside head tag are in your control, include base element. The BaseHref property is ignored in this situation.
This is by design.
For example, you can try the following code:
<html>
<head>
<title>Example of the BASE Tag</title>
<base href=http://www.CuteSoft.net />
</head>
<body>
<img alt="" src="http://cutesoft.net/uploads/21.jpg" border="0" />
</body>
</html>
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