I have owned numerous Miniature Horses and full size horses and the pony sizes in-between for many years and I still currently own a Quarterhorse and over a handful of the mini ones.. I do separate them and I am all for it.. AT LEAST in my situation..
I have a near bomb-proof, well mannered QH who is just as easy going as ever.. for anything and everything, except other horses, especially the minis. He can share a fenceline just fine, but I have had them in the same area before -when I was there, while cleaning areas, etc.- and this taught me, he does not respect them, so they are separated.
However, I had a 13.2 hh. pony (now deceased) he was in his 40's and he couldn't handle being turned out with my full size horses or even a smaller weanling or yearling full size.. so I bought him his OWN mini mare.. they were the best friends.. she stood beside him as he was put to rest.
Add to that, I also ran all of my stallions together, breeding or not.. all 3 of them.. and they LOVED the company of each other AND they were pastured beside mares and fillies of all ages with NO problems.. No flames..
I judge everything from what I experience.. but a majority of the time, I say NO to full size and minis together and stallions with stallions..
Added.. my stallions were raised together since weanlings and two of them were never used for breeding.. Unfortunately, two of my stallions passed away (along with some of my mares) when we had an unknown illness sweep my farm.. I can honestly say.. my stallion was happier with his buddies..
More so than the mares..
There are risks in everything.. but use common sense.