I spoke too soon. The WordList does follow the verse filter, and it already did that in PT8. But as indicated in the title of this thread, it’s the Find Similar Words tool (within the WordList) that doesn’t follow the verse filter, and it still doesn’t in PT9.
The project where this initially showed up has moved past this stage now, but I tried your suggested solution in another test project to see how it would work. I found that exporting the corrected wordlist from the auxilliary project and importing it into the base project doesn’t change the text of the base project. So it seems the only approach is to either ignore the spurious entries in the word list, or make the corrections also in the books we’re not working with, which largely negates the point of setting the verse filter.
Of course, another approach would be, after making the corrections in the auxilliary project, import all the NT books back into the base project. But that’s too dangerous for my liking – you would have to be very sure that no-one has done any work in the base project! So I won’t even suggest it!