adpstiom tobthe new threat is the big danger.
how many traveller planets would want to join the IoM though. They would be giving a lot up unless they join up under special conditions. And that decentralised command might actually aid the imperium since they wont need some high command at capital input and can act on there own discretion. The 3rd impurem all so has engramed operatives that can take over a person to assess and deal with new strange events. This will give a rather consistent response since it will often be the same person handling every first contact.
Want isn't really a factor.
Let's say you live out on the frontier, somewhere like the Sword Worlds.
A dreadnought shaped like a cathedral appears in the sky, run by a man with a very big hat with five names and a "I can do what I want" charter. He trades beads with you, you think that was weird, and then he goes and sells the information on where your planet is to the Ministorum for a tidy profit. If your planet is lucky, that's that, your planet is misfiled. If you're not, then a decade down the line ships coming to demand the Imperial tithe come. They burn your religious idols, shoot your defense force, and steal your sons and daughters, install whatever wealthy family surrendered first as planetary governor, and you find your grandchildren are being worked to death as your planet's biosphere is destroyed in order to feed resources to some foundry world that will not receive what it being taken for a generation.
This happens again and again until the information reaches a sector lord who is able to send a ship to warn the Third Imperium. The fastest ship possible would be a Jump 6 drive, meaning it can travel 6 parsecs per jump with each jump taking a week, but X-boats are generally Jump-4 and play relay. The Traveller Wiki says that it takes 4 years for an X-boat relay to get from Regina, the trade hub of the Spinward Marches, to the Imperial Core.
Eventually, the Third Imperium and allies will get their shit together, but the main factor is time. Traveller does not have FTL comms, and it's FTL is slow.
Everyone other then the Imperium of Man (and Tau) in 40k is fast. Tyranids can devour entire systems in the time it would take to warn them it was coming, Dark Eldar can wander out of their black city basically at random, Necrons can go "I don't remember a planet being here" and delete it if they're having a good day. And of course, Chaos.
I'm not saying it's an impossible task, just one that is stacked against Traveller's setting. Teaming up with the Tau can delay, but 40k's gimmick is that everyone's on a doom spiral, and Traveller doesn't have a lot of hard counters to the things that make them succeptable to the same.