I have used flake food in the Eheim auto feeder although I prefer to use pellets. If you do use flake food I would recommend that you don't fill it up and that you change it out regularly.
I do. I’ve been using it with a Neptune Apex auto feeder. I’ve had it in my feeder for a month and I haven’t had any issues with it clumping up or anything else. I did kind of crumble the flakes with my fingers to make the bits a bit smaller.
I also mix in some pellets. Interestingly enough, I find that my fish prefer the pellets over the flake food. However, once the pellets sink, they’re reluctant to eat them off the substrate or rock and then go after the flakes floating on top.