I'm not sure what you mean by this. If you mean a minion that isn't part of a custom group, technically no, every custom critter must be part of a custom group, but you can make a custom group with just that minion in it. You can use them in a "fight a boss" objective, (which you can't do with standard minions), which can be set to appear after another objective is completed. (example, when you click a blinky, the minion spawns.) If you want the minion to spawn in like an ambush, no, you can't do that.
Sorry, that was a bit unclear. I was referring to the random appearances of the critters. I wanted to design a couple of different customs for the same critter and it could prove some additional variety in the enemies being fought. But taking a closer look that probably just means random as in "random" minion from the selected enemy group. So disregard that question.
The file size limit is probably what I remembered from Live, I just recall encountering the limits while trying to expand my custom groups I believe.
Thanks for your answers, much appreciated!