Boot, alarm app and clearInterval

I intend to make timer app that can run in the background

Is there any chance you could just use/update the existing alarm app - since that handles timers too? You could then just make your app update alarm.json with the timers it wants scheduled.

Does that mean that the clearInterval effectively only applies until alarm.js is done?

Yes, that's right - because alarm.js either uses load to load another app straight away, or is displays a fullscreen message.

another load of alarm.js?

No, I don't think so... Once load(...) is called it's like a complete restart - it gets rid of everything and starts from scratch