@Oddant1 we sorted it out, there is a conflict of the /home directory in the container vs the /home on the cluster. So the workaround is to not bind the host file system (default is to bind it); then we rebind /home elsewhere:
singularity exec --no-mount hostfs --bind /home:/newhome $SINGULARITY_CACHEDIR/amplicon_2023.9.sif qiime
My feeling is this will need to be tweaked to get it working precisely, but just wanted to make sure to leave this here in case others run into it.