Your request doesn't actually make a lot of sense Harvey. You select an area, and THEN photoshop pulls the other layer - to where?
Since we are on the subject of Feature Requests related to Auto- Align. Here's a few …
• Locking the position of layers should be possible. Making the unlocked ones move to a fixed position defined by the bottom most locked layer. THIS woud be an improvement and perhaps make more sense, than what you have asked for?
• At the moment 'reposition' is not accurate! Two identical layers will not align accurately when 'reposition' is chosen. When Difference blend mode is chosen on the top layer, and at 100% you can see this clearly. Brings it closer, but its not doing what it should. Again a potentially useful new feature introduced, that has not been properly tested.
Well, photoshop would look for objects in each layer, that were similar to those in the selected area of the first layer and pull each layer to into alignment with the selected portion of the first layer. This would be very helpful when aligning layers with paralax by allowing you to choose a focal subject.
Just lockin a layer doesn't gain you anything. With all of the layers linked and their position unlocked you can move and reposition or crop as desired. Basing your descision on any layer in the group.
and pull each layer to into alignment with the selected portion of the first layer
Which is the 'first layer'? The first selected? first in the layers panel?
The first/top layer in the selected group would work fine for my purposes.