[BlueMage]

Assuming unmodified settings.txt file; the population affects every production aspect of a facility. This includes the ship yards, research/intell, and resource gathering systems. Basically, for every one of the (possible) 20 population modifiers you can change how much a bonus population gives in both ship yard rate and/or production of reasources (intell/research/min/org/rad).

If you want a flat rate; simply change the ship yard bonus to zero in the settings.txt for all the population bonus areas.