OK it truns out that the problem is simply that the nodejs root path has to be set. So the script used to start cryosparc from inside the container has to include
export PATH=$PATH:/app/cryosparc_master/bin:/app/cryosparc_worker/bin:/app/cryosparc_master/cryosparc_app/nodejs/bin
...
npm config set prefix /app/cryosparc_master/cryosparc_app/nodejs
cryosparcm start