Embedded linux is everywhere. But arguing that's a reason to use it, or not a reason to use a microcontroller / SOC is wild. Each has tradeoffs.

SoCs run linux everywhere. Good luck serving a configuration page over wifi from an atmega.

You're so stuck in your line of thinking. How about you run an API and host the client in a native app? Problem solved. How about you don't run sshserver. Problem solved.

I'll take linux in an appliance over having to install an app any day, but that's just me.

For me it's more about security. If I have a an appliance tied to the internet my entire network is susceptible. With an app, and bluetooth, I could just send data between the appliance and the iPhone, and then use the iPhone connection to the network to send data to the server (if needed / wanted but probably not for this application).