After Effects - Particular Rendering
I think you have answered your own question, but let me try to answer it from the perspective of a programmer (not one who wrote After Effects, but one who has written a lot of programs and seen a lot of source code).

After Effects (or any other compositing program) operates on layers.  Layers can be combined, masked, or used as inputs to transformations or operations.

The layer that contains your icon doesn't know about any processes or effects that come after it.  If you apply a particle emitter to that layer, particles will be emitted regardless of whatever masks come later.  Some particles may be masked by later layers/operations, but none of that affects what particles may be emitted due to the shape/color of your icon.

When you compose your icon with a mask, and then apply the emitter to that result, then of course the emitter is starting with the masked pattern.

Which is correct?  It depends what you want.  If you want to show lots of particles being obscured by a mask, the first is what you want.  If you want to show an alternative shape emitting particles, the second is what you want.