Ran the commands - output below (trimmed for the 5k text limit), TLDR - didn't work, still has the invalid key order on /dev/rdisk3s1. I'm guessing this means a reformat or at least a wipe and reinstall OS & data?
-bash-3.2# fsck_apfs -y -o -T /dev/disk0s2
** Checking the container superblock.
Checking the checkpoint with transaction ID 9338396.
** Checking the EFI jumpstart record.
** Checking the space manager.
** Checking the space manager free queue trees.
** Checking the object map.
** Checking the encryption key structures.
** Checking volume /dev/rdisk3s1.
** Checking the APFS volume superblock.
The volume Macintosh HD - Data - Data was formatted by diskmanagementd (1412.141.1) and last modified by apfs_kext (2142.120.7).
** Checking the object map.
error: btn: oid (590718), xid (9338352), type (0x40000003), subtype (0xb), flags (0x4) level (1)
error: btn: invalid key order: index 14 is greater than index 15 (should be less than)
index 13 key : b5 8e 06 00 00 00 00 00 6f 40 48 00 00 00 00 00
index 14 key : 40 06 10 00 00 00 00 00 a1 f2 36 00 00 00 00 00
index 15 key : ce a4 06 00 00 00 00 00 59 61 45 00 00 00 00 00
index 16 key : 5b af 06 00 00 00 00 00 38 8c 74 00 00 00 00 00
Object map is invalid.
** The volume /dev/rdisk3s1 was found to be corrupt and cannot be repaired.
** Checking volume /dev/rdisk3s2.
** Checking the APFS volume superblock.
The volume Preboot was formatted by newfs_apfs (748.77.4) and last modified by apfs_kext (2142.120.7).
** Checking the object map.
** Checking the snapshot metadata tree.
** Checking the snapshot metadata.
** Checking the fsroot tree.
** Checking the extent ref tree.
** Verifying volume object map space.
** The volume /dev/rdisk3s2 appears to be OK.
** Checking volume /dev/rdisk3s3.
** Checking the APFS volume superblock.
The volume Recovery was formatted by newfs_apfs (748.77.4) and last modified by apfs_kext (2142.120.7).
** Checking the object map.
** Checking the snapshot metadata tree.
** Checking the snapshot metadata.
** Checking the fsroot tree.
** Checking the extent ref tree.
** Verifying volume object map space.
** The volume /dev/rdisk3s3 appears to be OK.
** Checking volume /dev/rdisk3s4.
** Checking the APFS volume superblock.
The volume VM was formatted by apfs_boot_util (1934.141.2) and last modified by apfs_kext (2142.120.7).
** Checking the object map.
** Checking the snapshot metadata tree.
** Checking the snapshot metadata.
** Checking the fsroot tree.
** Checking the extent ref tree.
** Verifying volume object map space.
** The volume /dev/rdisk3s4 appears to be OK.
** Checking volume /dev/rdisk3s5.
** Checking the APFS volume superblock.
The volume Macintosh HD - Data was formatted by storagekitd (1934.141.2) and last modified by apfs_kext (2142.120.7).
** Checking the object map.
** Checking the snapshot metadata tree.
** Checking the snapshot metadata.
** Checking snapshot 1 of 1 (com.apple.os.update-3379F3DC95CFF07D9D49D5CE34EF1CCB1E66EF7D12A3055A5D1A0D2695C12EDE)
** Checking the fsroot tree.
** Checking the file extent tree.
** Checking the extent ref tree.
** Verifying volume object map space.
** The volume /dev/rdisk3s5 appears to be OK.
** Checking volume /dev/rdisk3s6.
** Checking the APFS volume superblock.
The volume Update was formatted by com.apple.MobileSo (1934.141.2) and last modified by apfs_kext (2142.120.7).
** Checking the object map.
** Checking the snapshot metadata tree.
** Checking the snapshot metadata.
** Checking the fsroot tree.
** Checking the extent ref tree.
** Verifying volume object map space.
** The volume /dev/rdisk3s6 appears to be OK.
** Verifying allocated space.
** The container /dev/disk0s2 could not be verified completely.