Heavy diatomic molecules have been identified as good candidates for use in electron electric dipole moment (eEDM) searches. Suitable molecular species can be produced in pulsed beams, but with a total flux and/or temporal evolution that varies significantly from pulse to pulse. These variations can degrade the experimental sensitivity to changes in spin precession phase of an electri- cally polarized state, which is the observable of interest for an eEDM measurement. We present two methods for measurement of the phase that provide immunity to beam temporal variations, and make it possible to reach shot-noise-limited sensitivity. Each method employs rapid projection of the spin state onto both components of an orthonormal basis. We demonstrate both methods using the eEDM-sensitive H state of thorium monoxide (ThO), and use one of them to measure the magnetic moment of this state with increased accuracy relative to previous determinations.