I reproduced the issue and came up with a workaround:

https://github.com/snapcore/snapd/pull/5974

The workaround may need additional fix for an unexpected situation
(where we need to reload snap-confine's apparmor profile after
generating the overlayfs snippet). I'm investigating that now.

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https://bugs.launchpad.net/bugs/1797218

Title:
  snap confine fails on top of overlayroot

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