Before choosing the bearing position you need to fix the gantry.

Separate tubes are weak.

You should have one large tube.

Your pros and cons are correct. There is no "best" for this design choice. They each have pros and cons. It partly depends on the other design compromises you make, for instance how much stick out the spindle will have due to other decisions.

If you choose good rigid gantry uprights, for example large tubes and not thin plates, you can get back the lost space under the gantry due to rails underneath.

For me, the hassle of trying to align rails in alternative B and the increased complexity and weight of the carriage make it not worthwhile. I prefer alternative A.