I've been doing it all along. While PokeFarmer is running is simply sit on my phone and evolve pokemon, giving me almost 100k xp/h at times. As well as managing my eggs of course.
But as the others have said, make sure to deny the app access to the GPS or you'll be spamming soft bans on yourself. They might be able to detect the double usage and give a permanent ban, but for now I haven't faced anything.