I feel like the idea is the more stable the fusion the more the limbs and number of eyes syncs up. All Garnet has going on Sapphire's third eye, both of them are watching.
You'll notice Opal only has two, but the four arms. I always took that as Amethyst trusting Pearl's judgement underneath it all, just hating being the subject of it, so she trusts Pearl to do the looking, and offers her arms as support.
This sort of falls apart with later designs, but I feel like the proper CG fusions at least are all designed with the relationships of the characters in mind.