From what I understand, the engines are still >$1m each, but coming down as they ramp up production speed and have radically simplified the engines with V2. The body is probably also much higher than the target range, but bearing in mind that it's just stainless steel and relatively well known manufacturing techniques, and not aluminium going through complex and expensive manufacturing techniques, they're probably well under any other typical rocket. I'd assume even significantly less than a new Falcon 9, which is already the low end of the industry in terms of price.
Another thing I'd bear in mind is that many of these ships never got completed, on purpose. There have been explicit "pathfinder" builds, but even with the "real" ships most never flew and were pretty much about working through techniques, tools, materials, etc. These won't have needed a full fit-out and will have been cheaper.
Edit: updated engine target from 500k to 250k
Keep in mind that the RS-25's cost $100m each. If it was atlas, the engines alone would cost $3.6B.
Edit: propellant is relatively cheap I believe. My understanding is <$1m per launch.
$44m per booster starts to sound like a more reasonable number.
I suppose that’s par for the course when bringing a previously lab-bound type of engine into practical use, but still. Did Merlin see iteration at such a pace prior to being fitted on Falcon 9’s? Raptor looks to be on track to be in a considerably more refined state when Starship goes into service than Merlin was at during the same point with Falcons.
But what you get at the end with something like 3000 parts in it's BOM, to something like 20 parts in the BOM, because most of the parts were deleted and integrated directly into the mold.
I suppose the better way to put it might be that Merlin's iteration was more in getting the production sorted out, whereas Raptor is iterating everything based on lessons from Merlin and previous Raptor iterations.
I think the issue you seem to be missing is that the marginal cost of materials that go into building a rocket is very low. The fuel cost is similarly a small percentage of the cost of building a rocket. The cost comes from the large workforce required and the low flight rate.
SpaceX has built and scrapped 17 Starships, 14 of them without even a static fire. They have scrapped four Super Heavy boosters, three of them without firing.
Test flights require fuel, planning, approval, and of course flight hardware. None of that is free.