My guess is partman-server (partman_base) is calling
minimize_extended_partition (probably command_partitions) which calls
ped_disk_minimize_extended_partition and it seems entirely intentional.

If I'm reading this right, then the behaviour is stupid.

-- 
if an extended partition contains unallocated space before the first logical 
partition, the start of the extended partition is moved to start of first 
logical partition [first EBR is MOVED and affected MBR and EBR tables updated 
when no such partition changes are requested] (present in both GUI and text 
installers)
https://bugs.launchpad.net/bugs/569201
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