I don't use SBS but would like to take a shot at answering for Mosh as a test of my understanding. If I'm incorrect Mosh will certainly chime in.
Results of SBS and custom footbed may be the same but they are different processes. Custom orthotic made by orthotist, podiatrist, whatever is made to neutral alignment of your foot. No discussion here as to whether it actually accomplishes realignment. However generally speaking that is the procedure and it is non-dynamic measurement method.
Mosh's SBS system uses dynamic testing of balance to find shims necessary to give you most stable balance, which will not necessarily lead to same alignment as neutral foot orthotic.
I don't use Mosh's system and have more to learn about it. However, I would say that if you are trying to correct pronation caused by injury but the pronation is not actually causing you another injury then Mosh's system may be more beneficial to your skiing.