After rooting or installing custom ROM, you will lose access to Apps that check for SafetyNet, e.g. bank Apps, some games like Pokemon Go, etc. Some devices may have work around, but it could eventually break one day and Google keeps making it harder to work around. Plus there are even some Apps that implement their own checking method to avoid root and custom ROM so that there isn't a general way to work around. If you need thoses apps, stock ROM is the best bet.