The idea in general is that by supporting the rights of nationalities, the contradictions between nationalities lessen, and all workers can join together in the (more or less) unitary workers state. So the point isn't really federalism, but rather democratic centralism/unitarianism through the unity of opposites within the working class. In this context the "right to secede" is a formal right which is never supposed to be used, but which is granted to make republics not want to secede. Although republics had the right to secede, the CPSU tried to support internationalist nationalism and discourage national chauvinism for most of its existence.

The issue is that when the issue of nationalities and the contradictions which it exists with is not handled carefully (which Gorbachov in particular fucked up spectacularly, although IIRC Kruchev and Breshnev could also have done better in this area (room for improvement for Stalin too definetly although he was a pioneer in the correct treatment of nationalities in socialism)) then the theoretical right to secede becomes a political bomb - especially ehen combined with national petite bourgeois elites from the shadow economy and right-deviationist (and disfunctional) economic reforms and political reforms which made politicians only dependent on national constituents.