Web.config inheritance happens even between different appPools.
If you want to stop this behavior, you should add the attribute enableConfigurationOverride="false"
to your appPool in the applicationHost.config file (located in %WINDIR%\System32\inetsrv\Config and %WINDIR%\SysWOW64\inetsrv\config) as in the following example:
<add name="MyAppPool" autoStart="true" managedRuntimeVersion="v4.0" managedPipelineMode="Integrated" enableConfigurationOverride="false">
<processModel identityType="NetworkService" />
</add>
Matteo