Theres a few reasons I recommend primary over fss0, none of them make it objectively better but just my recommendation.
Firstly, anecdotally is has fewer issues. Usually from my experience when people have problems related to games not working switch to fusee primary and its sigpatches fixes the issue.
Secondly its much simpler for support. By this what i mean is users generally dont know if they are using primary or fss0 and trying to get them to figure it out for giving support is a nightmare. Because of this on the discord servers I mod we tend to just recommend fusee primary, because it will cut down on support time and confusion by just having everyone use the same method.
Thirdly, it tends to have faster and better support. The sigpatches always come out for it before fss0 and a certain homebrew app tends to really not like fss0.
If you know what youre doing feel free to use fss0, this is just a personal recommendation not me saying fss0 is bad.
As for booting, usually I would recommend people swapping from sysnand and emunand use the hekate stock sysnand function and chainload emunand through fusee primary. If you want to use both sysnand and emunand with cfw you can keep one as fss0 or just keep using what works for you.