I think we've come to an amicable understanding, then. And of course, out of sheer impishness, I would say that if logical consistency is what you're after, why not try it through the context of an artistic framework? Time Bastard theory, for instance, might do better as an artistic interpretation. Because, after all, if logical consistency is the goal, then the particular interpretations you make do not matter, so long as they are all consistent with one another. Pursuing logical consistency is a bit different than codifying objective truth. I personally would never use Time Bastard myself, but for as stubborn as I am in defending the purity of the scientific method, here at the Compendium (where my efforts have probably annoyed many people) and elsewhere in life, I likewise take great satisfaction in the sheer diversity of inspiration people can take from the same piece of art. That's not to say I won't argue with an interpretation I disagree with, like Time Bastard, but it'd be a productive contention...you know, useful dialectic. That stands in contrast with the contention I have with those who attempt to pass off Time Bastard (for example) as a legitimate piece of science. Calling it that confuses weaker-minded people into all sorts of delusional worldviews about the form and function of science.
If, for the sake of logical consistency, you have to hold that the Entity is responsible for the Ocean Palace time gates seen in Magus' flashback, then, really, the best way to support that premise is to work from the top down, using the canon to provide aesthetic evidence on its behalf. For instance, does Truce really consist of five or so buildings? No. That's a game limitation. There's a whole town there, probably with thousands of people. How can I prove that scientifically? I can't. But aesthetically, it makes perfect sense. Yah?
Right...anyhow, I think you get my point, and I get yours. =P