As @Peter says, they're all grammatical, but it does make a difference where not, only, and also go.
The normal position for a logically salient piece of machinery like these words is right after the first auxiliary verb, which is the auxiliary verb that's required for some rules, like Question Formation, Negative Contraction, Subject-Auxiliary Contraction, and others. So the example sentence is the best one.
However, there are problems with these words. Only has a focus, and it can appear immediately before its focused constituent, or before any constituent containing the focus. The addressee can generally tell from the intonation contours what the focus is, but the reader can't, so in writing it's good practice to put only as close as possible to its focus.
In the case of the second sentence, only is sitting right before the verb phrase starting with been that is its focus, and also follows not, which is in its accustomed place right after the first auxiliary. Which is the position of also in the second sentence, so it increases the parallelism, as @Peter pointed out.
tl;dr your editor had it right.