In particular, this was an issue with the SteamWorks "contentprep" tool. We had to run it from the command-line as a post-build step, like:
python steampipe/ContentPrep.app/Contents/MacOS/contentprep.py --console --verbose --source original/Game.app --dest prepared/ --appid <our app id> --nowrap
The most important part is the "--nowrap" option, which disables contentprep from trying to add Steam's DRM to the app binary.