Maybe I'm looking at a tangent, but didn't the plot of CT came up as various people working on separates areas of it which then was pieced together at the end? Like how Kato worked exclusively, or almost so, on the Antiquity events. I'm not saying that because whoever was in the charge of the Cathedral events wanted to use one of the most classic paradoxes in time travel in a time traveling game should be the de-facto answer to handwave the inconsistency, or to stop trying to establish theories that can explain it and everything else at the same time.
But at the same time, won't this should be a sign that it may not be wise to take it that seriously beyond a certain point? After all, there doesn't seem to be other cases than the likes of the Marle Pardox. Like for example, once Magus gets sent to Antiquity and Melchior is imprisoned in Mt. Woe, he obviously didn't had time to finish the Masamune. By the same logic of the Marle Paradox, Frog's Masamune should've regressed to the Red Knife until the original got embedded in the Mammon Machine and was completed, but that wasn't the case. What I mean is, that if there is no consistency or repeated cases, then how can it be taken as part of the norm?
But in a way I can understand. The Marle Paradox is still a canon event whose implications and impact can't just be ignore due to that it played out, isolated or not. But again, I think it's more suited to be treated as an exception, rather than part of the rule. And this also goes for the theories created here.