In STO novel The Needs of the Many the Typhon Pact is a small trading alliance. The novel also handwaves away the differences between STO and the regular novelverse being that they're alternate realities, and one of the key differences is that in STO, there was no Borg invasion and final defeat in 2381. Thus implying that the Typhon Pact was planned as this small trading alliance, and cranked up to something much greater after Destiny.
No, that doesn't follow at all. First off, the "alternate timeline" rationale is just one book's throwaway conceit, not a universally accepted doctrine. Second, even if it were an alternate timeline, the divergence point would've been long, long before Destiny
, because ST:O disregards most of the events of the DS9 post-finale novels. And third, the Pact wasn't even conceived until after the Borg Invasion.
Bottom line, STO and the novels aren't alternate timelines, just different fictional creations made by different companies and creators who have different takes on the imaginary Star Trek
universe. The makers of STO pick and choose ideas from other tie-ins like the novels and comics and incorporate them as they desire, but there is no formal policy to treat them as alternate timelines and make sure everything fits into some vast multiversal logic.