It is a theory and I have to admit that I never thought about the Borgs that were left in the post-apocalyptic Earth, before StarFleet and all that goodness took place. But it doesn't explain everything, only that it is very likely that STD is an iteration of ST universe and it takes into account the multiverse by using parallel timelines. With the Sporedrive you are able to break the boundaries, and visit those alternate timelines, not just the Mirror Universe.
But, it would also mean that the Kelvin timeline is not going to happen in the STD universe, making TOS, TNG, DS9 and Voyager to be in the main, and all the rest has developed some other way. It would also mean that in Discovery's universe, Spock doesn't flee Romulans to another world, and get completely lost from the Prime Universe.
Nobody hasn't asked what is going to happen to Enterprise, once Discovery has jumped and it is left alone with unknown number of Control's ships? Is it going to be able to fight it off, or are the premonitions shown in this episode a sing that the Enterprise has no choice, but to follow, or then Discovery has to abort the jump and try to assist to win the battle.
I'm saying this because it is very likely that Section 31 blackships are armed at least 2 (n+1) phaser banks and a set of torpedo launch tubes, plus whatever weird gismos S31 has been cooking in the black labs/stealing from other races, or archaeological digs.
Here's the thing, however, since the Sphere Data is a sentient and seems to be aware of its presence, why is that Discovery/Burnham has to find a way to save it, when it could override everything they do and do whatever it wants. In a way it must be thinking that the Discovery is a downgrade or an upgrade to its old self, and therefore, it can continue cruising the space forever, observing the species etc.
All while it has done so, and they kind of confirmed that it has gathered AI data, and what happened to them along its lifespan - Why is that nobody in Discovery or in the StarFleet thought that they should make an investigation into the data to see if they could find a way to solve the current problem? What happened to the normal investigation procedures?
I see a few possibilities of how this could have ended, but recently I've allowed STD just take its course and allow me to go where they boldly head into in the classical sense of exploring the unknown.