I have `/usr/bin/env` in my "Macintosh HD" but not in the recovery partition. Is this normal?
Is it normal to not have /usr/env/bin in the recovery partition?


Yes, it's perfectly normal for /usr/bin/env to not be in the recovery partition.

If you were to mount the Recovery partition and open the BaseSystem.dmg container to search for the file, you'll find that it doesn't exist.

$ diskutil list

 #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:      GUID_partition_scheme                        *1.0 TB     disk0
   1:                        EFI EFI                    209.7 MB   disk0s1
   2:                  Apple_HFS Macintosh              999.3 GB   disk0s2
   3:                 Apple_Boot Recovery HD            650.0 MB   


So, disk0s3 is the one we want to mount

$ sudo mkdir /Volumes/RecoveryHD
$ sudo mount -t HFS /Volumes/RecoveryHD


Now, open the recovery system image BaseSystem.dmg.

$ open /Volumes/RecoveryHD/com.apple.recovery.boot/BaseSystem.dmg


A GUI will pop up on the screen with a Finder window.  



Traverse to the /usr/bin and you'll notice that env is not there.

 

It's important to remember that the Recovery partition is a slimmed down version of the actual base system.  To make rEFInd work correctly, it needs to be done on the boot partition, not from the recovery partition.  So, in the end, you didn't mess anything up.