The reason most land vertebrates have four limbs isn't because there's some advantage to it--the fish that we evolved from just happened to have four limbs. Similarly, there's no real advantage to having five fingers--our ancestors just happened to have five, and we haven't lost any. And remember, land vertebrates are a very tiny fraction of the animals out there. As for niches, most niches are created by other life forms. A woodpecker only has a niche because there are stationary trees that don't whomp them. Grazers exist because grass is sessile. While certain configurations would certainly be universal (again, cephalization; I'd probably include segmentation in this, as well as possessing some skeleton), I think those universals would be fairly limited, and fairly general. I mean, a race of centors is entirely plausible--all it would take is for the fish that crawled out to have six fins, rather than four. Monkeys with two tails are plausible. Four-winged birds actually existed. Mobile colonies in which each organism is highly specialized exist.
Life, in other words, is far more weird and wonderful than people generally think, and a sci-fi writer could blow people's minds just by showing what's already alive today. Alien worlds should be at LEAST as weird as what we share our biosphere with.