Why didn't they leave the train tracks on Mason flat instead of building that trough they are in? Will cars be able to use Mason once MAX arrives?

Why not leave the tracks flat with the road? Because it's safer, obviously. Just look.

Despite an early rash of cars getting stuck on the tracks along Mason St., BNSF railroad tries to minimize, in all cases, any location where a pedestrian or car could cross the tracks. The construction on Mason provided an opportunity for the city and the railroad to work together to save both time and money.

And seriously, who doesn't love saving time AND money?

There will still be plenty of opportunity to get that car stuck. Vehicles will still be allowed on Mason even after MAX service begins. So drive carefully out there.

If you're thinking it's still a pretty easy thing for pedestrians to hop over, you're right. The city is currently considering adding a decorative fence for the tracks that would place an even larger barrier between the street and the tracks.