Since I don't think it's possible to solve this issue on the LinkedBelts side (I still encourage you to report the SA+5Dim incompatibility to the developers of 5Dim if they aren't aware of it yet), I added a startup setting that will stop LinkedBelts referring to entities it doesn't create.
So if you enable that startup setting (before adding either SA or 5Dim's Transport, else it will crash) you should be able to play with SA+5Dim's Transport+LinkedBelts.
Let me know if there are any problems.
Do note that if 5Dim's is updated to remove the duplicate underground belt, or if they are loaded in a different order, the linked belt based on it might disappear, so enable the setting at your own risk.