It would be nice if the CLI updated that. But given your finding, it sounds like it doesn’t.
My understanding (based on creating GitHub - gregmsanderson/postgres-ha-timescaledb: Postgres + Stolon for HA clusters as Fly apps with Timescaledb) is those parameters are only set when you first create the postgres instance/cluster.
The good news is I found you can edit those parameters afterwards by doing a stolen update e.g I did this:
fly ssh console
export $(cat /data/.env | xargs)
stolonctl update --patch '{"pgParameters": { "shared_preload_libraries": "timescaledb"}}'
exit
… so you would change that to have your name:value in that JSON on line three.