opam: Fix 'opam init' error when relisting an opam instance

When relisting an opam instance and the opam root directory is already populated, the '--set-default' parameter must be provided otherwise the following error is reported:

No switch is currently set. Please use 'opam switch' to set or install a switch

Related to swh/infra/sysadm-environment#4971 (closed).

Also only capture stdout when calling opam list to ease debugging.