Not sure if you are referring to a tune for your car after you have put an aftermarket cam in your car, or if you are referring to a Ghost Cam Tune.
I will address both -
To put it simply neither are bad for the car (unless done wrong I guess)
A tune for a car with an aftermarket cam would just need a custom tune (or SHOULD have one I should say). This means that whoever is tuning your car whether it is MPT, Lund, or whoever else that does custom tunes, will just ask for what modifications you have to your mustang. As long as you tell them that you have an aftermarket cam, they will make accommodations for that.
A ghost cam tune is where your car does not have a cam, however, the tune programs the car to sound like one has been installed (hence the "ghost"). With v6 cars I have heard that MPT is the best (maybe the only right now since BAMA stopped selling theirs) ghost cam tuning company. Along with that tune is performance upgrades as well. Also, you should be able to request having a ghost cam with fuel economy/more low end torque/Hp. They are very good at what they do. With 8 cylinder mustangs I hear that LUND is the best (MPT also has one) provider of the Ghost cam tune. Both serve the same purpose.
It essentially makes the car have a lopey sound like the old muscle cars you see in movies
I honestly haven't looked into LUNDs tunes at all, so I am not sure if they can be loaded with SCT 4's but I would assume they can be. MPT does allow you to load a tune with your tuner for sure!
As for whether or not it is good for the car, I would say it is perfectly fine. I haven't heard of any problems with them - other than BAMAs when it came out - and they have been updated very nicely. Pros:
Sounds very nice
It is a performance tune
The "Ghost Cam" part is just for show (but it comes as a performance tune so not sure if this is actually a con)
I will add more if I think of any but another way to think of it is that it is just another performance tune that changes the way your car sounds. That's all it really is. If you like the sound of it go for it, if not there are other tunes!
Here is a video (skip to 35 seconds to hear it):