Why does updating ISPconfig always change my main.cf from postfix?
ISPConfig changes the configuration of services only when you select "y" for the question "Reconfigure services" during update. If you select no, then no config files will be changed.
In case that you decide that ispconfig shall not update your config files, it might be that new features introduced in ispconfig will not work on your server until you manually change the config files or that bug fixes that need a config file change will not work until you manually apply the fix.
So its totally up to you if you want to go the easy route and let ispconfig reconfigure the system or you want to do the reconfiguration manually.