This is not really an issue since it does not impact my usage of the phone. I run FP Open OS and I upgraded to Android 7 smoothly. However, I cannot deactivate the stock AOSP SMS app any more (could do it on Android 6 before). I do not use this app, I use Silence as a substitute, which has been set to default SMS app. So, that is why it is not a technical issue, everything works fine. This is more of a UI decluttering-issue (i.e. since it is activated, it is displayed on my application board).
I still can do it for all the other stock AOSP apps though.