How can I restrict a Flat Rate to a single product SKU?
It really depends on the context of the event. If that event is receiving an order by default, then your conditions either need to be based on the order (such as "Order contains a particular product") or you'd need to loop over commerce-order:commerce-line-items and evaluate line item based conditions via custom Rules components.

I'd give that condition I mention above a shot before trying anything more complicated, though.