Is there any advantages or disadvantages of having the T track go one way or the other?
Kind of like laying flooring, I would personally prefer t-tracks crossing the underlying supports (frame crossmembers) at right angles. But that doesn’t mean you can’t do it whichever way you prefer, especially if you have another layer of material below providing additional support. You can always try it one way and change your mind later with minimal relative expense. The beauty of a kit is that it’s yours to learn on, grow on, and customize as your needs/skills evolve. I’d be surprised if there’s still one subjective item on my machine that hasn’t changed since day 1.
Well i was thinking of a 3/4 inch BB So the screws would have some bite and two layers of MDF and if there going in the y direction access to the clamps would be from the front but if you’re going with x you could have more t tracks in use for better holding power 
Stopped using T tracks years ago. I find for me and my work I just side screw down all my materials and it works for 95% of everything I have ever made I resurface then swap the spoilboards when needed.
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I would recommend going in the X direction (left to right). I ran mine front to back and I use my cnc bed for sanding parts and the cord is always getting caught in the t-slot grooves. It would also be easier sliding clamps in.
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I would’ve never thought of that one!!
For doing slab work I prefer the y direction. All depends on your applications.
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I prefer to have them crossing on the short axis. It is easier to get the hardware in, and you can support longer boards at more places. T track running longwise won’t do any good when you need to clamp a 2x4 to the bed.
You probably will use t track for hardwoods more than sheets. So, think about fixturing small annoying stuff.
My final advice is that 6” spacing is fine for most of the bed, but having a small area of 3” spacing helps with odd/small parts and vises.
I have used both ways and like the X better first I have a 4 ft table and tee track comes in 4 ft length and it is easier to set up.
I’m still working on it