>>can we manage things like SnapMirror relationship creation from this System Manager?
yes, you can (without needing ONTAP CLI or other tools)
>> if it is possible to configure SnapMirror between FSx and on-premise ONTAP storage using only System Manager.
yes, possible.
Pl remember that , when you use SM from BlueXP for an FSx , you are using an embedded version of ONTAP SM tailored to the FSx instance. Here you can't configure physical components or some system settings. There are limitations in case of encryption mismatch and a few advance configurations.
AFAIK features like hardware diagnostics and cluster wide settings are not there as physical layer is managed by AWS. Also, there is limitation when you have multiple HA-pairs
