The advantage of being intolerat to some religion is that the religion sliders are zero sum. Therfore you can increase the tolerace of your main religion by being intolerant of some other one.
Eg. I conquor some muslim provence in N.Africa. I know I am there with nice garrisons for thirty years due to nationalism. I want to go to war with someone else, therfore I need low revolt risk in all my catholic provences, so I can absorb a lot of war weariness. I know the muslims are going to revolt anyway so I station garrisons there and do not need them in my core provences. In the mean time I send priests to convert them.
Eg. I conquor some muslim provence in N.Africa. I know I am there with nice garrisons for thirty years due to nationalism. I want to go to war with someone else, therfore I need low revolt risk in all my catholic provences, so I can absorb a lot of war weariness. I know the muslims are going to revolt anyway so I station garrisons there and do not need them in my core provences. In the mean time I send priests to convert them.