I found that the shifted y is only in the newest version of the scriptures. Think new maps edition or thin pages if you are referring to the book of mormon as a standalone. Since my wife recently gifted me a new quad, that's why I hadn't noticed any text anomalies because they weren't there. I have highlighted another verse that illustrates my point a little bit more clearly. The verse is mosiah 2:36. As you can see, starting with the fourth line, there is a divide with the left side of the verse subscripted and the right side regular. Line 4 is the most obvious because the fault line occurs in the middle of the word "ye." The second line "go contrary to" is left of the fault. This continues until the 9th line where the line contains no shifts.
My theory? I think this shift pattern is a result of either capitalizations or footnotes (notice how these make the line taller than usual) coupled with letters that go below the line (like p's or y's). If one line is abnormally tall in height and the line preceding it contains some low hanging characters, a predetermined line buffer may not be sufficient to avoid crowding. It appears that the new publication attempts to compress lines in sections rather than uniformly make a predetermined buffer for each line to solve this problem.
This theory does not clarify why in my original observation of Mosiah 2:31 the y is shifted. If you look to the very next line, there's a capital G which makes that line abnormally tall. The line with the shifted y has no reason to shift the y down to get even closer to the next line. To maintain the same buffer of space, if the publishers wanted to do any shifting here, it should have been up. This means that I am open to ideas for what is going on.
