You are generally paying for unlocked firmware that will run whatever code you want, a feature that pirates would target on retail consoles. IIRC, some consoles also put more RAM in development kits.
Maybe they're hoping to make a little money on the pirates...
It's certainly possible—and already done—with iOS.
Likewise, "homebrew" on such a system would probably be like iOS homebrew is currently: an ecosystem of open-source projects where users are expected to download, compile, and sign the binaries themselves using their personal developer certs.
The way this has been impeded on previous consoles is to encrypt retail executables and lock the key in some "secure" coprocessor. These obviously do eventually get cracked, but at that point the system is probably so thoroughly exploited that you can do everything with a retail console anyway.
With this setup, it could easily blacklist known retail binaries and refuse to sign them.
Nintendo accidentally showed a devkit with 64GB of internal storage rather than the 32GB you get on retail units.