I don't know the appropriate setup to encrypt whole disk drive using FileVault 2 and Automatically backup it without issues. Currently, I'm using a 2nd-gen Intel i7 MBP running macOS High Sierra 10.13.6 (17G5019), One Internal Crucial SSD, APFS volume, and using Time Machine for Backup on a G-technology External Drive, Mac OS Extended (Journaled).
/dev/disk0 (internal, physical):
#: TYPE NAME SIZE IDENTIFIER
0: GUID_partition_scheme *500.1 GB disk0
1: EFI EFI 209.7 MB disk0s1
2: Apple_APFS Container disk1 499.9 GB disk0s2
/dev/disk1 (synthesized):
#: TYPE NAME SIZE IDENTIFIER
0: APFS Container Scheme - +499.9 GB disk1
Physical Store disk0s2
1: APFS Volume Macintosh HD 456.0 GB disk1s1
2: APFS Volume Preboot 20.4 MB disk1s2
3: APFS Volume Recovery 512.0 MB disk1s3
4: APFS Volume VM 10.7 GB disk1s4
/dev/disk2 (external, physical):
#: TYPE NAME SIZE IDENTIFIER
0: GUID_partition_scheme *4.0 TB disk2
1: EFI EFI 209.7 MB disk2s1
2: Apple_HFS G-DRIVE USB 4.0 TB disk2s2
3: Microsoft Basic Data G-UTILITIES 4.1 GB disk2s3