There’s no clear winner between native and docker to run duplicacy web IMHO, but both are infinitely better than the Synology package due to the limitations you mentioned already.
I would still highly recommend the Docker route, it removes the need to handcraft a systemd config for the web service and makes it easier to set which account the service should run under (which is useful to avoid errors when restoring data and setting permissions). But, it does require a user knows how to setup a docker image in Container Manger etc. etc…