TM - yes those are the ones to comment out.
settlement population factor has many inputs:
Code:
<root>
<factor_modifiers>
<factor name="SPF_FARMING_LEVEL">
<pip_modifier value="1.0"/>
<city_modifier value="0.80"/>
<castle_modifier value="0.70"/>
</factor>
<factor name="SPF_FARMS_BUILT">
<pip_modifier value="1.0"/>
</factor>
<factor name="SPF_HEALTH">
<pip_modifier value="1.0"/>
<castle_modifier value="1.0"/>
<city_modifier value="0.8"/>
<pip_min value="0"/>
<pip_max value="25"/>
</factor>
<factor name="SPF_BUILDINGS">
<pip_modifier value="1.0"/>
</factor>
<factor name="SPF_TAX_RATE_BONUS">
<pip_modifier value="1.0"/>
</factor>
<factor name="SPF_BUILDINGS_FUN">
<pip_modifier value="0.5"/>
<pip_min value="0"/>
<pip_max value="25"/>
</factor>
<factor name="SPF_GOVERNORS_INFLUENCE">
<pip_modifier value="0.8"/>
<pip_min value="0"/>
<pip_max value="8"/>
</factor>
<factor name="SPF_TRADE">
<pip_modifier value="1.0"/>
<castle_modifier value="0.15"/>
<city_modifier value="0.2"/>
<pip_min value="0"/>
<pip_max value="20"/>
</factor>
<factor name="SPF_SQUALOUR">
<pip_modifier value="1.0"/>
<castle_modifier value="1.1"/>
<city_modifier value="1.5"/>
<pip_min value="0"/>
<pip_max value="40"/>
</factor>
<factor name="SPF_PLAGUE">
<pip_modifier value="1.0"/>
<castle_modifier value="0.75"/>
<city_modifier value="1.5"/>
</factor>
<factor name="SPF_TAX_RATE_PENALTY">
<pip_modifier value="1.5"/>
</factor>
the main negative ones are squalor and plague and tax penalty, the others boost it, so generally the population will continue to grow without the building bonuses.
the main limiter I found was squalor. The current <pip_max value="40"/> will effectively cap populations as it overwhelms just about everything.
Reduce to 32 and populations should find it easier reach the level where settlements will grow enough to be upgraded with population growth bonuses.