What exactly are you trying to accomplish or what do you mean?
Because when using Admin Backup/Transfer, the backups will include all domains. On the new server you can import everyting again with Admin Backup/Transfer. In that screen, you can define that you want to use the new nameservers.
So best is to first transfer only the admin account, then change nameservers, define the new ones. After that is done, go to Admin Backup/Transfer and setup the nameservers to be used on restore.
After that, restore resellers and after that customers.
That would be all.
If your new server has new ip's you do have to change the nameserver ip's with your registrar.
Admin Backup/Transfer is the tool with the least interaction.
The difference is that with cPanel you transfer accounts -from- the new server.
With DA you transfer accounts -to- the new server.
So also with Cpanel you still have to login to all the new servers, you still have to change the nameservers at the registrar. I don't see the difficulty or difference, sorry.
Hope somebody else can help you, because I think you will need to create a script for it to work like cPanel transfer.