They very much don't. STO borrows some characters and events from the novels, but that's all. Their storylines are wildly divergent. The STO novel The Needs of the Many hints that they're alternate realities in the same multiverse, but that's more of an easter egg and doesn't hold up to scrutiny. Spoiler: big huge novel spoilers showing how different they really are. Click at own risk!! -Data returned, but looks like a young Noonien Soong and is no longer a part of Starfleet. The plot completely contraricts his return in the STO-verse. -Dulmur and Lucsley's first names are different. -Deep Space Nine was destroyed and has been replaced by a new Federation-designed space station. -Sela, Donatra and Tel'aura are dead, the Romulan states are reunified and are part of the Typhon Pact. -The Borg are gone, and remain gone as far as the 31st century. -Andoria has left the Federation in the wake of the final Borg war. -The Romulans, Breen, Tzenkethi, Tholians, Kin'shiya and Gorn have forged an alliance known as the Typhon Pact. -President Bacco is dead.
Not really: Spoiler The millions of cubes and assorted infrastructure of the borg are gone - in the 24th century. That doesn't equate with the borg remaining gone until the 31th century. Not even close.
Sadly, you're actually mixing apples and oranges up with only knowing half the story (the behind the scenes story that is). Both series were launched with a uniform approach with the attempt to heavily pull from one another. When STO sales declined and they were forced to go Free to play, STO pulled a "We need to do our own thing to help generate sales" --- after a fashion, by that point, the uniform universe approach actually wasn't working out because of lack of communication and lack of speed in decision making, so STO kind of rightfully did what they had to do after a fashion. I knew at one point where the breaking point was (I followed the story line in STO, but never actually got in the game) and there was a fine point when the staffing changes occured that the shift in story continuity push changed. It was about the time Bill Roper left as VP and went to Disney, but I don't know what season of STO that physically was.
According to the writers themselves, STO merely borrowed some elements of the novelverse and there never was a plan for them to stay in continuity. Ask them yourself in the Trek Lit forum - they're not shy about discussing it.
As I remember, it only said the borg didn't assimilate everything by then due to 'endgame' which lead to 'destiny'*. I don't doubt 'destiny' was meant to the the final end of the borg. Just as Data's and Janeway's death were meant to be final in trek lit. But trek lit is a commercial product, and, like Data and Janeway, the borg are a well-known part of the star trek franchise. As such, Data's and Janeway's death was not final, after all. And the tentation to resurrect the borg in some form (let's say, even if they no longer have their massive resources and can no longer assimilate the galaxy) exists. *Of course, as per 'future's end', there are timelines in which the galaxy is not assimilated without 'endgame' happening. See above.
The problem with the Borg is that they have no allies, no friends, and are (or could become) a threat to everyone. They create the ultimate "Us vs. Them" scenario where all the races in the galaxy would eventually have to focus on eliminating the common Borg threat.
After all this time, why can't the Borg remotely override, and deactivate, Starfleet vessels defenses and computer systems like the Voth did to Voyager?
They do when they want to - see "Endgame" for when they do it to Voyager (and then just to hail Janeway)
The borg can give an impromptu call. NOT disable weapons (without command codes). There's a MASSIVE difference between the two.
Yeah I always thought there were significant differences between the two chronologies even before the game launched, at least going by the "Path to 2409" released mostly prior to said launch.