Alignment is important on partitions containing data, in order to maximise the chance that block operations will match whatever the underlying block structure is (4K on modern hard drives, more than that on flash-based drives).
Extended partitions don't contain data, they're simply containers for logical partitions. The only operation which is done on extended partitions is reading the single 512-byte sector which defines the logical partitions, and writing it when modifying the logical partition structure (so hardly ever). Because that operation only involves a single sector, it can never match a larger block size, so any writes will be sub-optimal and there's no way of improving that. The alignment of the extended partition itself doesn't affect the possible alignment of the logical partitions it contains, so there's no need to align it there either.