I think it would clutter the report too much to include the md5sums, but
doing

  md5sum --status -c /var/lib/dpkg/info/<package>.md5sums

for each package and adding a tag '[LOCALLY MODIFIED]' to the
Package:/Dependencies: field sounds like a good idea.

** Changed in: apport (Ubuntu)
   Importance: Undecided => Low
     Assignee: (unassigned) => Martin Pitt
       Status: Unconfirmed => Confirmed

-- 
apport should capture the md5sum of relevant files to detect local modifications
https://launchpad.net/bugs/70946

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