When the ball makes contact Flynn's arms do not make his "silhouette unnaturally bigger". But he's back into a natural silhouette only just in time. Before that he's stuck his arm out (instinctively? intentionally?) so may have been a pen by last season's rule.
I take "natural silhouette" does not mean arms touching side of torso or tucked behind players back. In this instance, facing the ball, legs slightly apart, the natural position would be with arms pointing down, slightly out from the body.
But, as a St Mirren fan, I'd be raging if it were the other way about. Having considered it I think the ref is right, but only because he didn't see it properly and didn't want to make a decision. And the linesman shat it.