As other comments have pointed out, there is no causal relationship between the use of JS and lack of accessibility, screen reader compatibility etc. So supporting no-JS and being accessible are two different concerns.
I'm absolutely all for accessibility and would never argue against making things accessible as part of some cost-based tradeoff. Frankly this shouldn't even be an issue that comes up if you 'just do things right' from the get go - but even if it does, the imperative is always on you to just fix it.
There might be a correlation where apps that happen to use JS are more likely to be written in a way which is less accessible by default, but that's another conversation.
With that out the way - totally agree with you, for certain apps with regulatory requirements insisting that JS not be required for use, that's what you do - and for good reason - max availability to anyone for public services etc - that makes complete sense.
The point I may have misunderstood is putting development effort into a SPA that only uses JS and works well with a screenreader versus the non-JS alternative that also works well with a screenreader.
Of course, it depends on where in the development process the developer becomes ‘aware’ of making the site compliant.
As you said, ‘do the right thing from the get go’.
A US college or university site can be sued for lack of Section 508 compliace.
So, it goes beyond development costs to legal risk of lack of compliance.
OTOH, a site selling cars probably does not need to worry about potential car-buyers using screen-readers.