As the title says… I really don’t know if it’s practically achievable.
I built a custom Samplerbox some years ago. It’s hooked up to a midi drumpad for live usage. After crashing some SD-cards in the process of building it I ended up making the SD-card read-only to prevent damaging it again. It runs from an overlay file-system as explained in this video. It’s been running for years now, always unplugging the Raspberry Pi without ever powering down. It still runs from the original SD-card. All samples and configuration files are stored on a thumb-drive. As you don’t save data to it playing live, there’s very little risk of damaging that one as well.
First suggestion: I know a Zynthian box is way more complex, but could it run from a locked SD-card?
Second suggestion: latency is always an issue. That’s why I made my Samplerbox run headless. This vastly decreased latency. Could this work as an optional feature for Zynthian? Thinking out loud: the system could check wether the ‘Back’ button is held down during boot-up. If so, the system doesn’t start X. Long-pressing ‘Select’ would have X fire up eventually or shutdown the system, whatever’s easiest to achieve.
Cheers,
Coen