I managed to get it to finalize the installation process (behind a reverse proxy with NginxProxyManager) using the full protocol:fqdn:port in the "External URL:" field (eg. https://www.example.com:443) .
After that there were issues with creating files and folders in its minio storage backend. I fixed those by changing the name of the container from the default pydio-cells to pydio. It seems that the pydio.gateway.rest hostname is hardcoded in the application and it fails to resolve the bundled minio nodes if you use another hostname, which leads to errors like:
2020-11-06T21:18:44.069+0300 [31mERROR[0m [32mpydio.rest.meta[0m Rest Error 404 {"error": "{\"id\":\"undefined\",\"code\":403,\"detail\":\"Unknown data source\",\"status\":\"Forbidden\"}"}
2020-11-06T21:14:04.292+0300 [31mERROR[0m [32mpydio.rest.tree[0m Cannot find DataSourceInfo for pydiods1 {"error": "Could not find DataSource pydiods1"}
The lead for the hostname idea is this post: https://forum.pydio.com/t/datasources-are-not-found/3223
Hope this helps!