1) There is a presentation titled "Anatomy, Modeling and Simulation of High Performance Vias: Why It Hasn't Mattered Until Now" on
https://event.on24.com/eventRegistra...epage=register2)There are plenty of video's on layer stack-up. Take those of Rick Hartley like this one
https://www.youtube.com/watch?v=ySuUZEjARPY and this one
https://www.youtube.com/watch?v=QG0Apol-oj0. Personally, I would ge for Gnd as reference.
3) So it is at least Gb ethernet? If the ethernet is just past through, then there is no reference other then the lines to each other (true differential pair, see Rick Hartley).
Make sure that the propagation delay (time delay) of the signals is the same. Via's add delay. If you route all on the bottom, chances are greater that all will have the same delay. SO, I would go for B. Do note that a through hole connector already has connections on both the top and bottom, so unless the SMD connector is on the top, you do not need via's.