Create encrypted partition for Time Machine from command line using diskutil or gpt, instead of Disk Utility?

Below (in the steps 1-5) I assume you already formatted some device as JHFS+ volume with an arbitrary name (in my example I use TMBackup). If you have an unformatted/unpartitioned disk, you have to partition & format it to JHFS+ first:

$: diskutil list
$: diskutil partitionDisk diskX GPT jhfs+ Name 0

or (if the disk is already GPT-partitioned with one volume):

$: diskutil eraseDisk JHFS+ Name /dev/diskXsY

The content of diskX(sY) will be deleted.

1. Get the devices list:

   $: diskutil list
   

   Example:

   ...
   /dev/disk1 (internal, physical):
      #:                       TYPE NAME                    SIZE       IDENTIFIER
      0:      GUID_partition_scheme                        *1.1 TB     disk1
      1:                        EFI EFI                     209.7 MB   disk1s1
      2:                  Apple_HFS TMBackup                1.1 TB     disk1s2
   

2. Choose the future backup drive partition and convert it to CoreStorage:

   $: diskutil cs convert diskXsY
   

   Example result:

   $: diskutil cs convert disk1s2
   Started CoreStorage operation on disk1s2 TMBackup
   Resizing disk to fit Core Storage headers
   Creating Core Storage Logical Volume Group
   Reviewing boot support loaders
   Attempting to unmount disk1s2
   Switching disk1s2 to Core Storage
   Waiting for Logical Volume to appear
   Mounting Logical Volume
   Core Storage LVG UUID: 586B5316-C702-4704-B8B9-D5F063AB1F84
   Core Storage PV UUID: 17373D1A-FCBD-4915-8699-3DA174B59BB7
   Core Storage LV UUID: AE765219-2012-4876-91DD-FE128DC8CA6C
   Core Storage disk: disk3
   Finished CoreStorage operation on disk1s2 TMBackup
   

3. Encrypt the logical volume (LV)

   $: diskutil cs encryptVolume $UUID(LV)
   

   Example:

   $: diskutil cs encryptVolume AE765219-2012-4876-91DD-FE128DC8CA6C
   New passphrase for existing volume:
   Confirm new passphrase:
   The Core Storage Logical Volume UUID is AE765219-2012-4876-91DD-FE128DC8CA6C
   Started CoreStorage operation on disk3 TMBackup
   Reviewing boot support loaders
   Scheduling encryption of Core Storage Logical Volume
   Core Storage LV UUID: AE765219-2012-4876-91DD-FE128DC8CA6C
   Finished CoreStorage operation on disk3 TMBackup
   

4. Set destination device for Time Machine backups:

   $: sudo tmutil setdestination mountpoint
   

   Example:

   $: sudo tmutil setdestination /Volumes/TMBackup 
   

5. Enable Time Machine

   $: sudo tmutil enable