In our cluster environment the job specific tmp directory is accessible through both $MXQ_JOB_TMPDIR and $TMPDIR. The first one doesn't exist in the local context, the second one points to /scratch/local locally.
With

remote-job-local-storage-prefix: $TMPDIR

files are copied to /scratch/local

Retrieving /scratch/local/fs/resources/rnaseq/ENCSR700EBI.fastq from storage.

while with

remote-job-local-storage-prefix: $MXQ_JOB_TMPDIR

files land in the correct location

Retrieving /dev/shm/mxqd/mnt/job/51813391/fs/resources/rnaseq/ENCSR700EBI.fastq from storage.