But I believe you're being far too pessimistic as to organizing it. The "omnipotent creature" to organize it just... city government. Roads and utilities are already built/managed well enough. You're right it won't "self-organize" -- the city has to contract and build it. It's paid for, like other large projects are, out of bonds paid off over deacdes by taxes, and/or contracts to operate. Nobody has to "outlaw the old system".
You just build it gradually, and UPS/USPS/etc. will take advantage of it wherever it can (for all addresses supported) because it will be by definition cheaper.
Governments manage big infrastructure projects all the time. This is how major bridges and tunnels get built. All of your arguments apply to pretty much most big government projects.
> Nobody is signing up for those taxes so they can get their pizza or Amazon delivery via a tube instead.
My point is that yes they absolutely will if it's cheaper in the end. Making up numbers, if you spend $400/year on last-mile shipping and delivery, it's financed by bonds up-front, and the extra taxes are on average $200/year/person for the next 40 years (but with progressive taxation)... then of course people would be signing up for that. Vastly better delivery service for half the price? Why wouldn't they be?