I've never done viewports. Just printing from what is in view in the model space. In this drawing, for example, I am creating two different views of the whole garden, one of each quadrant inside the fence, and two of each border garden, so 14 different ones in all and sometimes more, e.g., overlaying the drawing on the image.
So, for example, to print the garden in the upper right inside the fence, I will zoom window so that the fence defines the top and right side and the left and bottom include the walk as far as the letters. I f I use your method with zoom to extents checked, I get a PDF of the whole garden. If I uncheck that, I get the right selection, but tiny, like 2-3" on a side.
Each of these areas has a different manager, so we are trying to give each a drawing of their area. The border gardens take two because they are long and skinny and my cohort assembles them into one over and under.