The total wavefunction is a function of both electron positions. There is no phase between them. The wave function is also a function of the electron spins. The total wave function (both spin and spacial part) must be anti-symmetric. Although a clever experimenter could prepare a pair of hydrogen atoms which had specified spins, in most cases the total (spin) angular momentum will be random, and if the spins are the same then the spacial part of the wavefunction will be antisymmetric and one of the electrons will be forced into an anti-bonding orbital. In a spin 0 case, the spin wavefunction is ant-symmetric, so to spacial wave function is symmetric, and both electrons can fit into a bonding orbital. The attractive force between the atoms will depend on the spins.
You may want to look up the Woodward-Hoffmann rules of orbital symmetry, which predict the stereochemistry of reactions based on simple physical descriptions of the electron orbitals.