This has been rejected upstream, with the following comment:
"It's not really possible for Jamie to fix this, nor for me to do so (as
metacity maintainer; the only way to currently avoid it that I can think of is
to patch all applications in the universe to stop using override-redirect
windows). It'd be nice to be able to manage override-redirect windows to make
them stack appropriately relative to other windows (among other things), but
override-redirect means "override any management". We'd need some kind of X
extension to fix this."
I don't think that there's any way around this I'm afraid, so I'm
rejecting this bug. Sorry :(
** Changed in: xscreensaver (Ubuntu)
Status: Unconfirmed => Rejected
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allows applications to popup above xscreensaver (which is locking the screen)
https://bugs.launchpad.net/bugs/239
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