I assume it doesn't, and that includes R&D cost that can't be spread across a large number of other doses.

While a healthy portion is, ugh, profit margin

Often with these rare diseases, if there's a cure or treatment for it often they require bespoke drugs. Sometimes with specialty equipment designed and built just for that drug (or drug family). Ofc with rare diseases, they probably only make like 5/year or some shit so they never scale well. In some cases (like if there's a short shelf life), they even make the drug on an as needed basis, further increasing cost

One of these specialty 2 mil dollar drug might still cost an actual 1 mil to make taking out profit margin/R&D recovery costs.

No one has given you an actual reply just assuming that the manufacturing costs for the drug are low. Zolgemsma is a modified version of adeno associated virus and has to be grown under specific conditions. It costs $500k-$1m per production.

It doesn't cost that much because the company are making a hefty profit, of course. And much more profit off it in the US as per usual, the NHS pays considerably less

The deal struck [in 2021] with Novartis Gene Therapies, secures the drug for NHS patients in England at a substantial confidential discount and paves the way for the National Institute for Health and Care Excellence (NICE) to publish draft guidance recommending treatment with Zolgensma.

The terms of the deal mean that some young children that currently fall outside the NICE recommendation criteria will also be eligible to be considered for treatment by a national multidisciplinary clinical team (MDT) made up of the country’s leading experts in the treatment of SMA.

This means as many as 80 babies and young children could potentially benefit from the life-changing gene therapy a year.

But profiteering aside, the number in the final paragraph is your answer. Up to 80 kids in the UK per year, so up to ~400 in the US, ~500 for the EU. It's not a big market but the cost of drug development doesn't get cheaper just because the number of cases is small, it gets more difficult and more costly. And there's more than one drug company chasing the market.

None of that is a defence of Pharma. But it is inevitable under capitalism. Eat the rich etc etc.

It doesn't cost that much to manufacture. The costs usually come from the time and people to research and develop this drug over years of trials playa..