As for the Mass Shadow Generator, there is a very real chance that Bao-Dur will be assassinated by Traya's Sith before he can determine how to reactivate the MSG and brief G0-T0's forces on it. This is also assuming that he will be willing to cooperate with G0-T0, which might take some time and persuasion.
Bao-Dur is a suspicious and introverted individual, he prefers to take matters into his own hands and has some trust issues when it comes to large organizations (Militaries and corporations in particular). He despises criminals almost as much as he hates the Mandalorians, so G0-T0 would need to be very careful in approaching Bao-Dur. Kidnapped him isn't off the table, but it would make him unlikely to cooperate with G0-T0, and he's not the type to be broken by torture or threats. He has no family or friends to blackmail him with, and is more than capable of breaking out of most restraining facilities.
Bao-dur and G0-T0 both worked on the Telos Restoration Project. G0-T0 knows that Bao-dur works on Telos. How is Traya gonna know that, or the fact that Bao-dur even exists/ is still alive? G0-T0 won't have a problem locating Bao-dur, far before Traya does. He has Exchange contacts on Telos.
And honestly, it wouldn't be that hard to convince Bao-dur it's a good idea to pull the trigger on Malachor again. He had no reservations about it in KoTOR II (excluding the Exile). In fact, it seems he really wanted to destroy his mistake, erase the memory of all those deaths he had caused. Besides, G0-T0 just has to pull the "I'm aiding the Republic" card, and boom, Bao-dur is on board. He hates Sith, he'd be more than happy to see Traya dead.