Transparency Masks should appear in layers panel like Clipping Masks
I like how Clipping Masks show up in the Layers panel as a "<Clip Group>", which you can expand to see the object being used as the mask and the object being masked. However, Transparency Masks do not show up at all in the Layers panel; you have to remember to open up the Transparency panel to see and interact with them. In a document with a mix of Clipping Masks and Transparency Masks, this is really confusing and makes the Transparency Masks easy to forget about. You should make the Transparency Mask show up in the Layers panel like Clipping Mask.
Objects with transparency masks applied are displayed with dashed underscore in Layers. Does it work differently for you?