Thank you for the detailed explanation.

Since the underlying problem is that overlayfs is not (yet very)
namespace aware, this issue may be intractable.

Naive question regarding copy-up:  Do the files in the upperdir and
lowerdir need to have the same owner?  If not, could copy-up be amended
so that it behaves similarly to the copying of a root-owned file by a
non-root user?  Ie the ownership of the file in the upperdir could
change to that of the user doing the copying/deleting.

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https://bugs.launchpad.net/bugs/1617388

Title:
  When using overlayfs with kernel 4.4, some files cannot be deleted.

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