Consistent with the rest of the DFDL Spec, I took a shot and put clarifying language in that says the fillByte is used, but not specifying details on exactly how the fillByte's bits are used. However, the more general issue is there independent of the bit-order issues. The description of alignmentFill regions and how they are filled does not say anything about partial bytes.
A clarifying sentence in the table for the dfdl:fillByte property should probably say "When unparsing, if a region being filled is a partial byte, then it is filled with bits taken from the value of the dfdl:fillByte property in an implementation-specific manner."