I've made a couple end grain cutting boards, but never ran them through the planer to flatten them. I've watched a couple YT videos and believe it could be done, if you took precautions. However, for me, the risk outweighs the reward. I don't want to take a chance of ruining the board after I've put all the time & effort into getting it to that point.
For me, it's better to put the time & effort into getting a good flat glue up so that you minimize the flattening required. The last one I made, I took a lot of time to ensure my cross cuts were straight & square. I used cauls to ensure my final glue up was as flat as possible. A few minutes with my 6" ROS, working through the grits, 60 - 100 - 150 - 220. It didn't take long at all, compared to the time I had already invested. A lot of people use a wide belt sander and that would be ideal, but I don't have one and am not inclined to get one anytime soon.