It turned out Steam does not allow to upload two separate Mac builds - one for Intel and another for Apple Silicon devices. We can only use one build and it must be Intel, because it's compatible with all macs.
Will it be possible to create a universal "fat" build which includes both Intel+ARM NWjs exports? There is a discussion in this post (scroll to the end), but I don't see a solution.
You can create two launch options pointing at two different executable files uploaded to the same depot: one for the proper Intel version and another one for the Apple's thing. (check the steamworks docs here, you have to scroll to the 'Initial Setup for New SteamPipe Apps' section.)
Players then will be able to select which build to play.