For a quick solution, targeting API level 22 in your application will run on Marshmallow but should not need to separately request permissions from the user.
Better solutions will come along very soon as MX starts to support Android 6.0
Thanks Darryn. Thats actually what I did. At least I now have the confidence to tell my customers that for now thats just how it is. I have the same issue with iOS where users will answer No to the permission questions as they don't understand and think its safer to say no. Unfortunetly it stops the app from working correctly which results in support requests. So it would be a big plus if on Zebra devices it can be disabled via MX or just switched off. I'll check EMDK releases for it...