The difference is that the second time, the 3-Liner can only be rescued by the same person who rescued it the first time. For the 2-Liner, if your opponent rescues half, and then you play SoG/NJ on the other half, for example, you two are able to share the LS.
Usually, this difference makes no difference. However, I would say that in general, the 3-Liner is better because it doesn't give your opponent the option of basically giving himself a LS if he should exchange a half-rescued 2-Liner into his territory and then give the other half to you.
