Well, the stability of the fusion depends on the bond between the gems fused. Garnet is a fusion between two gems that have a very stong relationship so she is a perfect fusion. No extra limbs or anything (well, maybe the third eye but for all we know, normal sapphire might have three eyes)

Opal was a fusion between pearl and amethyst and what bonded them enough to fuse well was their need to protect steven (maybe the second time they fused too)

Sugalite is a fusion between sapphire, ruby and amethyst. It’s a lot more monstrous than opal and this might indicate that either ruby or sapphire don’t like amethyst very much. (Evidence could be garnet making a joke about “keeping” amethyst, making fun of the fact that she was created by the kindergarten) 

Now, Malachite. The fusion between lapis lazuli and jasper. It is a beast. Like, a straight up monster. This is because lapis and jasper hate each other.

Now, if all the gems on homeworld were to fuse, it would be some twisted body horror. because not all gems like each other and not all gems are humanoid. The centipeedle is a gem, remember?