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Answering my own question (and showing my ignorance of PowerShell/Windows):

There were two things missing in my original script. First, I needed to pass the /S (Silent) flag to automatically accept the defaults, and second I needed to pipe the output to Out-Null so that the install script would wait until the EnergyPlus installation was complete.

Here's the important command:

"& $env:ENERGYPLUS_DOWNLOAD_FILENAME /S | Out-Null"