I think so. This option only changes the button prompts on the screen. Playing The Phantom Pain with the XBOX prompts while using the DS4 was a bit annoying.
Ok, that's how it should be.
But honestly why it's annoying?
In past few months I've helped friends upgrading their pc (basically installing a fresh w8.1, installing cheap capable gpu and installing SPC driver with a Bluetooth stick to support their DS3/DS4) instead getting a PS4 and after a few hours of Rocket League (or other games) they completely understand every button prompt.
The only reason to need PS button prompts are of course it looks nicer and for absolute new beginners.
Project M 3.6 was the only game (beside Gamecube/Wii emulation) where I try to change the buttons with Playstation ones because that actually can confuse people (try to let a new player get out of the game in Smash with a non Nintendo controller) but that's a minor thing and there is a fix for it.
We should unite and ask devs to implement a switch for implementing DS4 button prompts!
That should be easy to do.
A 360 pad, DS3 and DS4 are basically the most used pc pads.