The universal remote should work just like a Roku remote - the Roku device shouldn't even know you're using a universal remote. I don't think you can use the app as a remote to enter the remote sequence, but an IR universal remote should work.
If you're using a Harmony remote all bets are off. Logitech/Harmony likes to have single key presses produce multiple presses which will mess things up. I guess it's possible that other universal remotes do the same thing.
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