Get a git diff without taking index into account

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Some background.
I'm trying to use Git as an object store for trees.
I put trees into the repo and can retrieve them.
I'm having issues with diffing these trees that I retrieve from the repo.
If I use a "git checkout" the diffs seem to work but if I create the
tree myself user lower level ls-tree and cat-file commands then the
diff doesn't work.
It seems to take the index into account.

Below is a complete working example.
Should be able to copy / paste line by line.
I am trying to run the diff of form:
  git diff [--options] <commit> [--] [<path>...]
where it says it does a diff from working tree to a commit

Maybe git is interpreting my command as one of the other forms?
Can someone help me understand what is going on?

#
# EXAMPLE
#

# cleanup and create dummy data
rm -rf /tmp/mydatastore && mkdir -p /tmp/mydatastore
rm -rf /tmp/test /tmp/test2 && mkdir -p /tmp/test/d1 /tmp/test2
echo "this is f1" > /tmp/test/f1
echo "this is f2" > /tmp/test/d1/f2

# create a new branch called test with data from /tmp/test
git --git-dir=/tmp/mydatastore/.db init --bare
git --git-dir=/tmp/mydatastore/.db hash-object -w /tmp/test/d1/f2 /tmp/test/f1
echo -e "100644 blob c837441e09d13d3a0a2d906d7c3813adda504833\tf2" |
git --git-dir=/tmp/mydatastore/.db mktree --batch
echo -e "100644 blob
11ac5613caf504eec18b2e60f1e6b3c598b085eb\tf1\n40755 tree
055f1133fbc9872f3093cca5f182b16611e6789a\td1" | git
--git-dir=/tmp/mydatastore/.db mktree
commit_sha=`git --git-dir=/tmp/mydatastore/.db commit-tree -m "initial
commit" c427094b22e74d1eaeebdc9e49e6790b5b6a706a`
git --git-dir=/tmp/mydatastore/.db update-ref refs/heads/test $commit_sha

# why does this show diffs?
git --git-dir=/tmp/mydatastore/.db --work-tree=/tmp/test diff $commit_sha

# after doing a checkout somewhere else it doesn't show any diffs
git --git-dir=/tmp/mydatastore/.db --work-tree=/tmp/test2 checkout test .
git --git-dir=/tmp/mydatastore/.db --work-tree=/tmp/test diff $commit_sha

# remove the index and it shows diffs again
rm /tmp/mydatastore/.db/index
git --git-dir=/tmp/mydatastore/.db --work-tree=/tmp/test diff $commit_sha

# it was my understanding from "git help diff" that this form of diff
is supposed to
# compare a work tree against a commit or branch and not take into
account the index.
# Clearly it takes into account the index because we get different
results with and without it
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