Darktable isn't really set up to do this. A lot of modern workflow software like this is "opinionated" — it's set up with a certain way of doing things in mind, and designed intentionally around that, rather than providing a toolbox of options. In Darktable's case, that workflow is non-destructive editing — basically the opposite of what you're going for.

But that said, in this particular case, there's an easy way to do things which is similar to what you're asking for and should give decent results. Import all your images in whatever way you want (darktable *.jpg on the command line), and make all the changes to each one. When you're done, enter $(FILE_FOLDER)/$(FILE_NAME) as the output, select all the images, and then press export. You'll need to check "overwrite" each time (but not for each file separately), presumably as a safety feature.

I don't think that Darktable has a way a to match JPEG output quality to input quality, though, and for the kind of thing you're talking about that might be a deal-breaker.