All these assumptions about planet bombing fail to take into account the most obvious and most important aspects:
If a war that has only been on going for 30 years or so, how can single colony ships repopulate an entire planet within that time frame? How can this happen on a regular basis? Also, if a neutral planet is colonised has no original inhabitants, where do the militia come from and who are they loyal to? Assuming that planets get completely wiped out and repopulated so frequently makes absolutely no sense at all.
Game play only makes sense and fits into the lore if you assume that planet population represents population under your control and registered for taxation. It does NOT just represent population alive. When bombing occurs, many die but the rest are unaccounted for because the infrastructure has been destroyed. Capturing the planet means taking the inhabitants under your control and registering them for taxation. This takes time, this is what 'growth' represents. I doubt that it means that Humans breed like insects in this universe.
This is why moving your government to onboard a starbase means that you cannot lose a planet through bombing. The aim of bombing is to destroy the government and inflict terror, not destroy the entire populace or something equally preposterous.
Also, if enemy culture causes you to lose control of a planet, it becomes neutral. Now if you recolonise, the population will be 0. This doesn't mean that they spontaneously committed mass suicide for no reason (Wail doesn't count) the population is still there but no longer under control.