Hi Cagney,
You can write your settings in the "maxstart.max" file. It´s located in "\Defaults\MAX". And if it is not there you can write your own. Just reset max do some customized settings like an own viewport layout an save it to "maxstart.max". Ok, this will not effect the existing scenes because you´re right in that the layout that is saved in the files. But at every start max will load the maxstar file.
Hope this was helpful