well it is better to mask via a layering method because you have more control on the mask channel itself, but i still prefer to use the side input. only problem is you cannot mask a precomp by using the side inputs of the nodes because it will only mask that one node.
on another note, i did find a way around that precomp issue with masking. if you end your precomp with a "lookup" node, it will let you mask the entire thing, but you have to invert the mask.