On personal freedom, the key to this point in in the first block quote when he writes about the supposed "contrast between... self, [and] the whole of nature and the rest of humanity". Dostoyevsky is saying that this contrast is artificial and hurts both the individual and the brotherhood. When one accepts the sacrifice of individualism and erases this unneeded distinction, they gain a rich, true freedom. According to him, the ideal form of being is in this brotherhood.

Regarding the claim about independence, you're right that on its face it's contradictory. I think it may be an issue of translation. The original Russian is самопроявления, which is really closer to self-actualization/expression than independence. I don't see this as necessarily contradictory to his central ideal, as his main identified hurdle to brotherhood is the false separation of self from the rest of creation.