I don't recall the station being 3-4 stories. I'll have to look next time I go there.
The Miami-Dade County building is just next to the Brightline and that has Metrorail and MetroMover tracks 2-3 stories up, but I've never noticed the Brightline being elevated. Could be, but I've never noticed
The station has a small street-level lobby. You go up a long escalator to the second level where the waiting rooms, retail, and food is located. When the train arrives, you go up another long escalator to the platform to board. The ceilings are expansive, which is why I was thinking it was the 4th floor. But, the trains are located on the 3rd floor.
Here's a construction photo. The three Brightline/Virgin track are closest to the bottom of the image. The tracks in the middle are Tri-Rail. (See below.) The track coming in off the curve at the upper right are Metrorail.
Photo Courtesy:
https://www.thenextmiami.com/tri-rails-aggressive-schedule-get-service-downtown-2q-2018/
There are existing tracks already from just north of the Brightline station to Port Miami, but I'm not sure what the gymnastics would be to send a train over there. They currently have shuttle service to the port, and that may actually be the most expeditious way to move folks. The bridge to the Port is literally only about 6 blocks from the station.
In order to get up to the station, there's a long incline that starts right after the I-395 underpass. In order to get from the Miami Central Station to the new Port Miami station, a train would have to go all the way past I-395 and stop before reversing to change onto those existing tracks into the port.
If I have my geography correct, the track that curves down and exits the bottom of the above image goes to the port.
Definitively some train gymnastics there. Because of that, I'm guessing any trains bound for the port will skip the Miami Central station entirely. But, who knows at this point.
On the Boca stop, we already have a regional train service (Tri-Rail) which services Boca Raton but it terminates at MIA, not downtown.
I'm not sure when it is scheduled to be completed, but Tri-Rail is expanding to Downtown Miami.
http://tri-raildowntownmiamilink.com/
In this image taken from the above linked site, you can see the relationship of Tri-Rail to Virgin trains. Obviously it's an old image because has the original "All Aboard Florida" name. But, I'm guessing it's still fairly accurate. This image does not show Metrorail, which would be to the left side of all of this.