Depending on the Hamiltonian parameters, two-component bosons in an optical lattice can form at least three different superfluid phases in which both components participate in the superflow: a (strongly interacting) mixture of two miscible superfluids (2SF), a paired superfluid (PSF) vacuum, and (at a commensurate total filling factor) the super-counter-fluid (SCF) state. We study the universal properties of the 2SF-PSF and 2SF-SCF quantum phase transitions and show that (i) they can be mapped onto each other and (ii) their universality class is identical to the (d+1)-dimensional normal-superfluid transition in a single-component liquid. The finite-temperature 2SF-PSF(SCF) transitions and the topological properties of 2SF-PSF(SCF) interfaces are also discussed.