Unless you are mining different algorithms or different coins, there is no good reason to run separate instances.
Not to contradict you here, the only reason why I started doing it was because I have complete mix bag of cards. I have everything from 1070's to 750ti's, but, mostly 1060s.
If I ran those all together it would crash at different points, so through my various resolutions one that I found to be productive was running separate instances of the different cards, 750ti x2 on one instance and so on up the line. Now, to be fair, with overclocking and other various reasons, I've never gone back and recombined them into one instance.
I just went back in and combined the 1060's into one instance, I left the 1070 separate and 750ti's have been removed for lack of space.
tl;dr.
Just wondered if running the separate instance and having the difficulty run lower was I hurting myself.
