A few of the issues as I understood them from before:
SE tribes could build on SE, then invade Island servers without risk to their base (drawback was, they could not bring the dinos back to SE with them)
Possibility of unbalanced fights with the new SE creatures against Island creatures
The above points are particularly relevant to players who do not have the expansion
With today's changes
The drawback of raiding Island servers from a base on SE is removed (albeit with a 12-hour cooldown)
Now you also need to worry about balance in the other direction
Players without the expansion are still stuck with the same issues, but now SE players may be able to breed Island dinos off-server to bring back
Should be an interesting weekend