hi,
1- sorry the configuration you are mention it is not correct, you need to remove the ground, select it and chose open boundary. and there is no need for the Free space layers.
2- the via is correct for the short option in one condition it should be between the two layers metal you are using for antenna.
3-the internal port will not affect you accuracy, it is simply says that the feeding point is not at the edge of the conductor, but I believe you should use differential port.
if you want me to check it please update the project and I will check it.
hope that I helped you.