Root cause analysis:

                (user-partitions (append
                                  (auto-partition disk #:scheme scheme) 
                                  (create-special-user-partitions
                                   (disk-partitions disk))))) <---


(define (create-special-user-partitions partitions)
  "Return a list with a <user-partition> record describing the ESP partition
found in PARTITIONS, if any."
  (filter-map (lambda (partition)
                (and (esp-partition? partition)
                     (partition->user-partition partition))) <----
              partitions))

I think create-special-user-partitions and the form above is automatically
trying to keep existing UEFI ESP partitions of the user.

And partition->user-partition failed for (existing) fat16 partitions.

So the fix of adding fat16 was definitely the right one for that specific
file system type.

It should be fine now.