It seems that the node position on the chart in all situations is calculated from the center. Until there is no other implementation, the only way to achieve a βalignedβ appearance is to use a suitable width.
digraph left { graph [rankdir=LR splines=ortho] node [shape=record] l1 [label="A\l|B\l"] l2 [label="C\l|short\l" width=1.3] l3 [label="E\l|long long text\l"] l1 -> l2 l1 -> l3 }
leads to the following: 
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