Your axes size includes the axes and labels. You are just comparing the white canvas, but you need to take into consideration all the components of the axes when sizing your plots.
The point being when you call yyaxis left, it needs to add a y-axis on the right side of your axes as well, and since the size of the uiaxis was set when you placed it on the app canvas, it has to use up some of the real estate on the right hand side to add it, making the actual plotting area smaller.
To correct for this, you need to adjust the footprint of the uiaxes in the Design View in app designer.
