The short answer is there isn't a supported way to use the deployanywhere from the bootdisks. That functionality is moved to the console exclusivly.
The issue you will have with the 3.x standard tools is you need to add the DB to boot disk because it isn't included and there isn't a built in option yet to include it. If you are willing to do some legwork the following could be done.
The DriverManager64.exe is also included in the standard tools but there is no built in driver database but I suppose if you are just building your DB as you go you could do so using the built in DA components and build your own DB of drivers. You will have to then create a custom boot disk that includes your driver db. And then like 2.5 you will need to run deploy anywhere manually. It will have to point to the correct location as the DB location will be your custom DB that you manually add. Or you can map a drive to your 3.1 console it has a built in database.
I hope that is a helpful start for you if I find a better document I will cross post it.