I didn't see the kind of identity between gravitational and matter fields with that of God that you saw in that paper. To me, it seemed like the author was trying to show that matter has no temporal origin, but rather it is only organized temporally and causally due to the temporal scalar field.
Although, there appears to be theistic implications in the paper. For example, if the time scalar just prevents everything from 'happening' all at once, then time does not explain why things in spacetime had to happen at all. This leaves either randomness (which is not an appropriate answer since who can accept that all these things in spacetime is one huge coincidence), or some type of lawful order that requires spacetime things (events, actions, evolutionary processes, stellar creations, etc) to 'happen' in the 'first' place. This lawfulness to the universe could be identified as God.
So, although I am not sure what the author's metaphysics say about the cause of spacetime events, I gather a theistic implication to it.
On a scientific level, I thought it interesting that not much was said about QED and QM along with the standard model. Might that mean that he cannot quantatize his GR driven theory of time in a manner that is suitable to quantum theories? Also, I didn't see much mentioned about special relativity with the non-simultaneity of events. How does a time scalar fit in with SR?