The idea that one can distinguish the 'thesis' and 'theory' of intelligent design is puzzling. While I don't have access to Jones' Encyclopedia of Religion, there's an entry from 2003 (listed as 'forthcoming') on Dembski's list of writings on ID. Note that this is pre-Kitzmiller, and is typical of Dembski's writings of the time - Sagan, Paley and Kant. Assuming that this is substantially similar to the final version, there's nothing about thesis vs. theory.
Beyond this, John Carter appears to misunderstand the idea of "theory". There are I think perhaps several other areas of what might be called "theoretical biology," such as parts of astrobiology, which also have a total lack of any hard evidence to indicate that they even have something real to study, in that case alien life. No. That's not what theoretical biology is. Take a look at the TOC of the Journal of Theoretical Biology. Or try Acta Biotheoretica. Or even check out the journal Astrobiology. Theory isn't about "things that lack total evidence". 
This entire section about 'thesis' vs. 'theory' of intelligent design appears to be based on both a misunderstanding of what Dembski was saying (pre-Kitzmiller, when he was predicting the overthrow of "materialistic" science and a department of ID at a major university within a decade) and a fundamental misunderstanding of the difference of what constitutes theoretical biology, and how it differs from unfounded speculation and science fiction.