Confusing, isn't it? It seems to me Panes and Album Thumbnails and Panes and Thumbnails are fundamentally different than the other thumbnail View As settings. The thumbnails represent albums or tracks respectively, and do not stack. At least I haven't seen them do so. Because we're used to stacked thumbnails, some of us expect to see them stacked when we select Group By (artist, for example). But no, that just affects how the thumbnails are arranged.
I'm sure the reason for this is stacked thumbnails are used for filtering in the thumbnail views. You can drill-down by double-clicking on them, or jump another category using links that appear on hover. In the pane views, the panes are used for filtering. I suppose the idea is providing two methods of filtering would be confusing, and might cause conflicts. I haven't thought that one through, and I'm not even sure how things have changed since MC12. I think this does warrant some consideration, however. In other words, would it be possible and practical to allow the option of stacking thumbnails in pane views in the same way they will do so in thumbnail views?
If I had the choice, however, I would probably use Panes and Album Thumbnails as is—without stacking. A small change I would like to see is groups to be separated from one another (e.g., by heading and/or horizontal rule).