‘Scale’ always means multiplier. Most of the ‘Scale’ variables in BaseLightmass.ini are to implement the various quality levels (Medium, Production). So for example NumHemisphereSamples * NumHemisphereSamplesScale gives the number of requested rays in the final gather. IndirectLightingQuality further scales up this setting.
Your calculation of total samples using NumHemisphereSamples * NumHemisphereSamplesScale * IndirectLightingQuality is correct. IndirectLightingQuality does affect a few other things though that also increase the build time.
Unfortunately I have not done enough investigation with the photons to understand exactly what is going on to answer a question like this. The phantom lights happen because not enough photons were gathered to estimate lighting. Increasing NumIrradianceCalculationPhotons and IndirectPhotonSearchDistance will both increase the number of photons gathered, which is the right direction. However there are several steps in there and I’m not sure which one is the problem (direct photons, indirect photons, irradiance photons).