Apple does this by sending an imposter user agent from Safari on iPads.

If only that was expanded to iPhones, too. And then send rotating, or randomized user agents.

For example, almost every major Japanese book/comic site uses canvas in their e-reader

You can fingerprint the originating TCP stack with some degree of confidence. If the request looks like it came from a Linux server but the user agent says Windows, that's a signal.

Likewise, the IP address making the request has geographic information associated with it. If my IP address says I'm in Romania but my browser is asking for the English language version of the page... That's a signal.

Similar to basic IP/Geo, you can do DNS and STUN based profiling, too. This helps you catch people that are behind proxies or VPNs.

To blur the line, you can use JavaScript to measure request timing. Proxies that are going to tamper with the request to hide its origins or change its fingerprint will add a measurable latency.