Getting back to the original question, there's a source that explains how the Union of Border Worlds came to be. It's called...um...it's right on the tip of my tongue...oh yeah, WC4.
Seriously, the Border Worlders decided to establish a nation of their own becuase they felt that they were being treated like second class citizens and that too much political power was resting in Terra.
The question of whether they were independant or not prior to that is interesting. In the TPOF novel, Blair and the Border Worlders advance the idea that since the Border Worlders had never signed the Articles Of Confederation, they were independant. Paulsen counters that by saying since the Border Worlds had been settled from existing Confed Worlds, and were integrated into Confed during the war effort, they were de facto Confederation worlds. I lean towards that view myself, but it seems that Confed did recognise the Border Worlders' claim to independance post WC4, as they're shown as a seperate nation on the WC

map.
In the context of WC4, and the plan to create a war between the two, it probably didn't make a huge differance. As Blair says in the TPOF novel, if the Border Worlds were an independant nation, then they were as a nation responsible for the attacks that "they" (read the Black Lance) were carrying out against Confed, which would form the basis for an all out war against them. On the other hand, if they were a part of Confed, then they were sheltering and supporting "terrorist" attacks against Confed, which would allow the Confed military to crack down on them. Either way, the Border Worlders were screwed.
Best, Raptor