After sitting down and going over everything I know about this fic, I believe I've gotten a substantial way towards solving its puzzles. The long version is at my blog here, but here I'll just state without justification the prediction I've come up with:

Voldemort believes fate won't let him defeat Harry until Harry attains the power to vanquish him, which in this case means becoming powerful enough to destroy all of Voldemort's well-hidden horcruxes. And in fact, Harry will become that powerful, by using the differing conservation laws for magic and science to conduct conservation-law arbitrage. Voldemort's plan is to possess Harry once Harry has attained ultimate power, but Harry will prevent Voldemort from winning through complicated means involving multiple currently yet-to-be-fired Checkov's guns.