Is it true that we often use 'not' with a verb or auxiliary verb i.e. 'not to do', 'do not need to do'? 'not' does not have this limitation when it forms a fixed collocation with other words, such as 'not...but...', 'not only... but also...'

1. The second fact is that many linguists work not just on languages other than English but on languages which have been little studied or not studied at all.
2. If this project fails, it will affect not only our department, but also the whole organization.

But I came across this sentence today.

a. In the discussion of (3) above, we observed that, although we analyse clauses and sentences individually for convenience, in real language they do not occur in isolation but as part of longer texts.

In my view, it should be

b. In the discussion of (3) above, we observed that, although we analyse clauses and sentences individually for convenience, in real language they occur not in isolation but as part of longer texts.

What's the difference between a and b? Is a formal?