Thanks for providing an example. With this sample data, there are a couple things going on. One is that there are a lot of potential box plots. There are 2 levels for P1 X 24 wafers X 13 lot IDs, so Graph Builder is allocating space for 624 box plots, which makes them skinny. However, a little less than half of those combinations contain data, so it only draws 290 box plots. That's still a lot, and I can see why they look too skinny since half the slots are empty. Looks like your data may have even more empty slots.
The only remedy I can think of is to create some synthetic variable that represents only non-empty combinations, such as the Wafer ID in lot ID column in the sample data does, but that may give up the consistent coloring.