It's hard to say, because we don't have enough information. The "code" you shared looks like it's part of a PowerShell script, or maybe it's a cmd script, which maybe they're executing from BuildMaster? Or they could be executing the process directly? Where does $targetInstances and $targetDatabase come from?
if they're just running a PowerShell script, then I guess they should just edit that powershell script as you suggested?
Can you just ask for the deployment plan? Unless it's v4 or earlier, it will be in OtterScript (a text file), and once you see it, it should be fairly clear how to change it.