There is (still?) a bug with indirect lighting though in 2.77 abf6f08 (Win7 x64 Pro, 32gb, i5 6600).
The linked file has 2 cube and 2 render layers, one for each cube.
Layer 1 has a diffuse cube that's being illuminated by a sun lamp and bounces it's indirect light onto the ground.
Layer 2 has an emission cube that's bouncing it's light onto the ground.
In the compositor, which should be open after loading the blendfile, is a splitview for putting the render layers 1 and 2 side by side to show that both contain all indirect light eventhough the cubes are only rendered on their respective layers.
To be clear about the result I'm expecting and not getting: by having the diffuse cube on the 1st (left) layer am I expecting blender to only render this cube's indirect bounced light and not also the indirect emission light of the cube from layer 2 (right), and vice versa am I expecting blender to render only the emission cube's indirect light on layer 2 (right) and not also the indirect bounced light of the cube from layer 1 (left).
So I'd say that indirect lighting is indeed not respecting the visibility of the layers although a bit differently than the original reporter described.