MakePE supports this too. Just like adding Adding Extra Files to WinPE, the process is the same. If there are files you need added to all ISO’s that are created with WinPE, just add it to the MakePE\Optional\ExtraFilesISO\All directory.
If you have content that should only go in WinPE 5 x86 and x64, then place the files you want in MakePE\Optional\ExtraFilesISO\WinPE 5
MakePE will handle the rest.