Thomass-MacBook-Air-2:~ root# diskutil list /dev/disk0
/dev/disk0 (internal):
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:      GUID_partition_scheme                         500.3 GB   disk0
   1:             Apple_APFS_ISC                         524.3 MB   disk0s1
   2:                 Apple_APFS Container disk4         399.0 GB   disk0s2
   3:                 Apple_APFS Container disk2         2.5 GB     disk0s3
   4:                        EFI NO NAME                 1.1 GB     disk0s4
   5:           Linux Filesystem                         91.8 GB    disk0s5
   6:        Apple_APFS_Recovery                         5.4 GB     disk0s6

# So the Stub partition is the 2.5GB Apple_APFS Container. The identifier is
# disk0s3. As a result to rerun the installer I had to execute the following
# command to remove the old stub partition. Afterwards I can rerun the installer.

diskutil apfs deleteContainer <identifier of the 2.5 GB Apple_APFS Container>

Or in the above example:

diskutil apfs deleteContainer disk0s3