Currently, to easily contain one’s brush strokes to a cel, one can set the Ink mode to “Lock Alpha”. However, this is unintuitive and means that one can’t mix it with the Shading Ink mode.
I think alpha lock should be a layer property with its own icon in the layers list, so that this can be quickly toggled per layer as needed. This is how it is done in Krita, Photoshop, and probably some other software.
When a layer is alpha-locked, you also cannot erase from it, the background colour is used instead (I suppose in Aseprite’s case, this could be transparent :]) I’d prefer this behavior in Aseprite as well.
While I’m here, an unrelated issue: I wish I could set both Subtract Selection and Eyedropper to Alt. Eyedropper is pretty much never useful when using selection tools, but if I assign both to Alt, the Eyedropped received priority. Would be nice if conflicts like this could be made context-sensitive and favour the more relevant option.