I think it really does depend on your environment and goals as to how you glue it together. Look into the POST script sections of your SC configs to see when you can call external scripts. It is possible to script out what you need and have SC then call the script to complete your clone, you can also install the SC agent on your clone host and have SC execute scripts on the clone target directly. The only advise I can give is to look into snapdrive and see what it can do. For example it might be simpler to call a snapdrive command to connect a flexclone to a vm via RDM instead of invoking the vmware/netapp api directly.
I'm not familiar with the inner-workings of SMO to tell you yes or no. I think a lot of folks using SC have a handful of custom post scripts that will help mount their clones, and then another set of custom post scripts to do application/database recovery.
It might be the case that instead of writing a script to do these activities, you could just call a snapdrive/snapmanager cli command, so your post script would be to call a snap product. This works well in somes cases and would save you some time, but may not work for others.