One of the best reviewed functions I wrote at work is a 2000 line monster with 9 separate variable scopes (stages) written in a linear style. It had one purpose and one purpose only. It was supposed to convert from some individual html pages used in one corner of our app on one platform into a carousell that faked the native feel of another platform. We only needed that in one place and the whole process was incredibly specific to that platform and that corner of the app.
You could argue that every one of those 9 scopes could be a separate function, but then devs would be tempted to reuse them. Yet, each step had subtle assumptions about what happened before. The moment we would have spent effort to make them distinct functions we would have had to recheck our assumptions, generalize, verify that methods work on their own... For code that's barely ever needed elsewhere. We even had some code that was similar to some of the middle parta of the process... But just slightly didn't fit here. Changing that code caused other aspects of our software to fail.
The method was not any less debuggable, it still had end to end tests, none of the intermediate steps leaked state outside of the function. In fact 2 other devs contributed fixes over time. It worked really well. Not to mention that it was fast to write.
Linear code scales well and solves problems. You don't always want that but it sure as hell makes life easier in more contexts than you'd expect.
Note. Initial reactions to the 2000 line monster were not positive. But, spend 5 minutes with the function, and yeah... You couldn't really find practical flaws, just fears that didn't really manifest once you had a couple tests for it.
Deeply nested code, especially with many functions that are called once, is really horrible to debug.
Extract functions when you see obvious repetition, not just to appease some dogmatic abstraction goal. Incidentally, this also helps the CPU (cache locality).
Along the same lines, I'd rather have a directory with several dozen source files than several dozen nested directories that may contain only one or two files each.