I think its a bit of a mixture of both, there is a 'standard' stat line with a standard points value, and adding or subtracting stats will increase the points by various amounts, some stats are given more weight than others. Then after that, any special rules are factored it.
It is worth remembering though that every army functions differently as a whole, which is why you won't really find a perfect mathematical balance of points/stats across all the armies. What is good value in one army might be fairly worthless in another, so thats where the arbitrary point comes in.
I assume GW also playtests the lists a fair bit before release and modifies it if something is too weak or powerful, though there often isn't strong evidence of tis in the final lists...