Thanks for your feedback.
Changing the active build configuration during build time has already been implemented in the in-browser client (the LiveSync toggle in the Build wizard) and the command-line interface (the --no-livesync switch). We have put it on our roadmap for the extension for Visual Studio and the Windows client as well.
We have logged persisting the active build setting per project for the Windows client and the VS extension for fixing in a future release. Thank you!
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