This is what bug 772472 seemed to be about initially (re. its original summary and the initial comment), but during the discussion on IRC we found out that Fernando was experiencing a different issue.

So, even without layer groups, the Align tool is current unable to select anything but the top-most visible layer at the click location. This works fine in many cases - what you see is often what you want to handle, similar to the Move tool - but fails if this is impossible, due to a layer being covered completely.

Workarounds are to make layers invisible. This is annoying, as there is no temporary or easily reversible way to do so.

A possible way out could be to introduce a "pick layer / choose active layer" tool option like for the move tool. Shift-Click, Move tool's modifier for toggling this, is taken by the Align tool already. 

One could argue that Shift-Clicking to select non-continuous slices of a set is uncommon, though (compare to spreadsheet applications, where Ctrl+Click takes this role -> maybe we should change Align's modifier key, and introduce a "pick active layer" similar to the Move tool.


Interaction could be like this:

- click: depending on the tool option, either pick the top-most or active layer (just like the move tool)
- shift+click: toggle the tool option, pick as above
- ctrl+click: add a layer to the picked ones taking the option into account
- shift+ctrl+click: toggle the tool option, pick as above