IIRC, Roddenberry really had no say in what novels got published or what disclaimers got put on them. And I think he felt that they
all violated the spirit of Trek. OTOH, he also thought that Star Trek II violated the spirit of Trek, so I tend not to trust his judgement too much about what the "spirit of Trek" was in the 1980's or beyond... While on the subject of Gene, that remark of his about how the machine planet V'Ger encountered might have been the Borg homeworld has never made even the least bit of sense to me--not only did V'Ger not come back to Earth intent on assimilating its Creator or anything else, the simple fact of the matter is that the Borg never had anything like the technology that V'Ger did...
IMO, the best Star Trek novels tend to be the ones that are later contradicted by "canon" material--and usually the "canon" material winds up being inferior to the novel that it contradicts. And, really, you can't blame the novelists for taking a few liberties from canon--because their novels are dismissed as non-canon before they've even figured out what they're going to be about! At least Trek authors know that going in, unlike the Star Wars authors that have had to watch Lucas increasingly invalidate their work with every prequel he makes...
In the case of the planet-killer possibly being designed to fight the Borg... the bottom line for me is that it makes about as much sense as any other theory of why it may have been created. Being from a non-canon novel doesn't make it any more likely than any other theory--but it doesn't make it any less likely, either, because any theory on why the planet-killer was created is "complete B.S." from a canon POV...