I admit that I cannot see the point of having ambient and flash exposure compensation settings tied together. Yet, as I have discovered, they are tied together by default on some Nikon cameras.
When I see how some vendors approach exposure compensation, I really feel like I've been pushed back in time where if I want to control things, I have to do everything completely manually. I'm going to use the word "dumb" to describe this. When we as photographers choose to engage with compensation, we are typically doing so for a reason, and with intent. If we are already mixing ambient and flash in a single exposure, it is also probable that we many wish to apply different levels of compensation to the ambient settings and the flash settings.
On some Nikons, the D750 and D4s leaping to mind, the flash compensation menu offers two options, entire image with two little icons representing ambient exposure compensation and flash exposure compensation and "background only" with only a single icon for ambient exposure compensation.
Reviewing the manual for the D4s I have in hand as I write reveals a section in the otherwise excellent manual that is nearly useless. If you want flash exposure compensation and ambient exposure compensation to operate independently, choose "Background Only'. I will call this vaguely intuitive and leave it there.
Also if you want the shutter to drag in lower ambient situations, you will likely have to change the setting in the Menu option called "Flash Shutter Speed" to a long shutter time, such as 30 seconds if you want full shutter drag capability. This does not mean that the shutter speed will BE 30 seconds, only that it will go that long if needed to make a successful ambient exposure while using the flash. Do not confuse this with the "Flash Sync Speed" which is where you can set the shutter synchronization speed for the flash.
Why a company that does such a brilliant job at Fill Flash with their Creative Lighting System makes this so convoluted is beyond me. Once you have the settings the way you want them, the cameras work beautifully, but check your own cameras as not all Nikons operate the same way.