According to requirement DFDL-12-011R:

"To avoid ambiguity when parsing, optional elements and variable-occurrence arrays where the minimum number of occurrences is zero cannot have alignment properties different from the items that follow them. It is a schema definition error otherwise."

I created a sequence where the middle element is optional. The alignment settings are different from the settings of the element that follows. I do not get the Schema Definition Error that I would expect based on the requirement above.

See test alignmentOptionalElem in the following files:

daffodil-test/src/test/resources/edu/illinois/ncsa/daffodil/section12/aligned_data/Aligned_Data.tdml
daffodil-test/src/test/scala-debug/edu/illinois/ncsa/daffodil/section12/aligned_data/TestAlignedDataDebug.scala
daffodil-test/src/test/scala/edu/illinois/ncsa/daffodil/section12/aligned_data/TestAlignedData.scala