Tl;dr: NO opting out once in; before plebiscite, subgroups are identified and given lands. FPE is a nation of citizens, not a nation of nations. Anyone who wanted to opt out would have to do so before their controlling geopolitical entity voted, after would be too late.
The only way that they would be able to do so was if they petitioned Peter to recognize them as a separate country. He would have no reason to do so, as he was using every erg of political savvy to increase the influence of his office. However, the point was made that the plebiscites would have to held so as to allow the actual groups present in each country hold their own plebiscite. Basically, his commitment was that whatever body you held loyalty to voted and gained admittance to the FPE as one body, but no body could force any other body in. It had to be done that way to prevent old resentments from tearing the whole thing apart.
Once a plebiscite had been held and you were accepted, there was no leaving the FPE. The constitution was held up by threat of military force and ratifying the FPE constitution was a irrevocable act.
A few examples might make things a little more clear. Take the native north americans. They are a separate nation that is wholly contained within the borders of the USA. The USA plebiscite would not obligate them to join the FPE, although the USA might have to give up land to the NNA's as a part of their "entry fee" regardless. If the natives petitioned the FPE to be recognized and held a plebiscite, the USA would not be obligated to join the FPE, but the FPE might declare that some land previously claimed by the USA actually now belonged to the "nation" that had just joined it and as such would be treated as sovereign territory, to be defended by the FPE military might.
Another example would be the Basques in Spain. If Spain wanted to hold a plebiscite, they would be denied until they agreed to allow the Basques some territory and a plebiscite of their own. This might have resulted in a few "pocket nations" that hadn't voted to become apart of the FPE, but all of them must have fallen over the course of the next thirty years, since the USA was described as the lone holdout during Peter's anisible conversations with Ender, and we know he died with the world united under his rule.
Source: pgs 100-102, 185-187. 190-191, of the paperback Shadow of the Giant. Card made the point that once ratified, the constitution would not be struck down or renegotiated.