If you would like to modify any IIS settings on role config, you can have start up tasks to do so.
For example as described in the article create a command file with the following command (bat file or cmd file) and configure it as start up task
appcmd.exe set config -section:system.applicationHost/sites/siteDefaults.limits.connectionTimeout:"00:03:00" /commit:apphost
Configure tasks up task.
<WebRole name="WebRole1">
<Startup>
<Task commandLine="Startup.cmd" executionContext="elevated" taskType="simple">
</Task>
</Startup>
Hope it helps.
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