It all depends when you actually call the functions you have added in your AutoSPInstallerFunctionsCustom.ps1 (assuming all your custom script is actually wrapped up in functions). AutoSPInstaller should only be loading (dot-sourcing) your custom functions into memory until they are called somewhere within AutoSPInstallerMain.ps1 (which you would also need to modify). However if you just have loose code in AutoSPInstallerFunctionsCustom.ps1 then yes it would get executed very early on - but you shouldn't.
Brian
Brian