How to edit the primary shape inside area in Allegro PCB editor ?

You mentioned that you need to align inside the boundary of the shape. For this, you can use shape edit boundary command which redefines the boundary of the copper area shape or its voids. You can define the new boundary inside or outside the old boundary.

Move into Shape Edit Application mode first and enable Shapes in the Find filter. Select any shape,press RMB and select 'Edit Boundary' option. Choose the 'Type' under Segment Type options which can be Line,Line 45,Line Orthogonal, and Arc. After choosing the Segment Type, you can select anywhere on the shape boundary and move the segment with help of mouse cursor even inside the shape boundary and then select the second point upto where you want to edit the boundary. If you want to align it with another shape as seen in your case, you can select the Segment Type as Line or Line 45 depending upon the boundary of shape chose in marked area and then try this command.

Let me know how it goes for you when you try this.