I *think* that this has not much to do with the different ways you're
launching ubiquity - the debug log shows that the preseed file has
definitely been applied successfully by casper - and a lot to do with
the second scenario having been run after the first on a disk that's no
longer blank.  lvm2's udev rules are going to have brought up all the
LVM volumes they can find on the system, and nothing in ubiquity takes
care to bring them down again before partitioning.  (Of course it's also
possible that there's some kind of race that means the two ways of
starting ubiquity behave a bit differently, but it doesn't look like
anything very fundamental.)

Try something like this as a workaround?

  d-i partman/early_command string vgchange -a n

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https://bugs.launchpad.net/bugs/1386153

Title:
  Inconsistent behaviour between 2 ways of launching Ubiquity

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