Hmm dunno if I agree w/ completely weakened.
After all, initially Tsukasa only offered small wildlife like frogs, after inanimate things got rejected. It shouldn't be that easy to break the seal of a completely weakened supernatural.
And I'd honestly have to reread to be sure but I don't recall the god's powers gradually recovering either.
Now, it doesn't come as a surprise that the god's power is correlated to the amount of sacrifices made. So while in the original timeline the god got almost buried and forgotten, that seemingly didn't happen in the new timeline. As for why, you made some elaborate guesses, but until we get to know more (if we do at all and they don't simply reset, which I don't expect) they'll remain just that, at least to me.
One thing I can agree on, is that this timeline's "god" is certainly more powerful though. Whether that is due to sustained sacrifices over the time or just a recent development though, I'm not sure: A "pile" of corpses would have decomposed over time if accumulated slowly, yet if a number of persons went missing in a short time that might raise unwanted suspicion.
More importantly though, assuming the clock keepers only changed the "recent" past concerning the Yugi twins, that would be a few decades ago, not centuries.