Question 1-2:
The differences between the related sequences and the blast search results are that the latter

- searches only the non-redundant databank, i.e. you get fewer duplicate entries
- retrieves also recent results that did not yet make it into the crossreferences
- does not always use the same options used in defining the related sequences.

Ad. 3. Go here for a view of how the combined results might have looked like. Homology is TRANSITIVE, i.e. if A is homologous to B, and B is homologous to C, then A is homologous to C (given that the A, B and C are homologous over the whole sequence length).

Ad. 4. This is another example of one way streets. The D-Ala D-Ala ligase picks up the carbamylphosphate synthetase subunits, but not the gluthathion synthetase (i.e., the search converges without the gluthathion synthetase being identified as a match). However, the gluthathion synthetase used as a query picks up both the D-Ala D-Ala ligase and the carbamylphosphate synthetase already in the second iteration.