I added your feature request to the Blast interface (http://aclame.ulb.ac.be/Tools/blast.html
After submitting multiple sequences, the result page gives on top the Query sequences
Now, next to it, there is a switch to MGE view
link. Just click on it and the results will be displayed based on MGEs hits distribution.
For each MGE, the list of query and hit sequences will be shown in the table side by side + the ACLAME annotations for the hit sequences, whenever available.
Let me know if this fits your needs.