What's the difference between status effects with the random flag compared to status effects with the separate flag?
Random does 1 of the selected effects chosen at random, separate treats each effect on it's own so there's a chance of inflicting all the selected effects.
If I understand you right, given that the default seems to be a 25% chance of inflicting a status after using a damage skill,
random means that out of X status effects, each has a 25/X% chance of occurring, but only one will happen
separate means that out of X status effects, each status has a 25% chance of occurring, so the chance the target escapes unscathed is (3/4)^{X}.
However, the interplay of these with the to-hit formulas is rather puzzling. I remember changing eye gouge to grant 3 status effects with the formula (MA+40)% as the hit rate. On separate, the display showed a 15% chance (or 45/3) to hit, causing the goblin to repeatedly miss his attacks.