Samus takes up 4 tiles in a 2 by 2 square, so given that the space between the columns (or whatever you wanna call the floating vertical pieces of the terrain) is three tiles wide, she would be off-center no matter what. What doesn't make sense is that there are five tiles to the left of the platform she's standing on and four to the right. If they had just extended the platform one additional tile to the left and adjusted the left column accordingly, it would've been perfect.

The only possible explanation I can think of is that having more empty space to the left might encourage players to go that direction first and thus find the Morph Ball right away.