Yup, can confirm that. About 50% of the time (Sometimes it works when I just rebooted my Surface), Opera ignores the Surface pen. Only touch input works as expected.
I'm running Windows 10 10586.218 on a Surface Pro 4, too.
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Greetings, I must say, Opera is without a doubt running buttery smooth on my Surface Pro 4. It's a good substitute for Microsoft's Edge, which unfortunately doesn't support extensions yet.
However, there's a thing that has been bothering me so far. It's Opera's bright user interface, which isn't a pleasure to use at night. After a while, I just gets tiring on the eyes and hinders productivity by a fair amount. Are there plans to bring a dark theme to the browser? Or can I somehow theme it myself without having to build it from the source?