It depends on the scope of the Federation "federal" government. Most likely, when a planet joins the Federation, it cedes much of its foreign policy and armed forces to Starfleet, whilst retaining local governance in most areas. I'm sure that on Vulcan, laws governing treatment of Pon Farr are not mandated by the Federation Council. They don't really need to be.
I also think there is no basis for comparison. Federal states exist in the real world due to large geographical or demographic size (or countries with a number of cultures within them). The US as an example probably has more federal/sub-national units than many other federal countries, yet has never shown signs of crumbling due to federalism per se. yes, there was the Civil War, but the principal issue (but not exclusive as all know) was slavery.