Yeah, valgrind is a bit noisy always because we are building the cache
in memory before (1) writing it to the disk and the write includes
unused regions and (2) we are hashing the entire thing before writing
it, including the uninitialised bytes. So that means while we do have a
few uninitialized bytes, it's actually safe.

This bug is fairly strange. Especially git vs packages. The only thing
different when building via git is that hardening flags are not used.
You could export those:

  DEB_BUILD_MAINT_OPTIONS=hardening=+all dpkg-buildflags 
  export CXXFLAGS LDFLAGS CPPFLAGS

but I seriously doubt that's the problem (if git always worked instead of 
always failed, this might have made sense).
If I had a user account on an affected machine, where

If I had a user account on an affected machine (it needs to be
reproducible by creating a fake root directory, and copying etc/apt and
var/lib/apt to it, then I can use -o Dir=$PATH_TO_FAKE_ROOT instead of
needing root), where I can build apt and have tools like valgrind, gdb;
I could (try to) debug that myself.

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