It kind of depends on what you need out of the model. I would generally align the axes to fit the “board” because it makes it easier to apply textures correctly and I usually want some sort of report such as a cutlist from the model. Any of the tools thatmake those sorts of lists can only report bounding box dimensions so if I were running a cutlist on your model, the rafters would report as much larger than they are.
There are some times, though, when it makes sense to wait to change the axes for a component. For example, when I modeled the leg for this workbench I drew the first one in place at the front left corner. I left the axes aligned to the model axes so I could use Flip Along >Component’s Red to make the front right leg. After I was finished make that copy and flipping it, I changed the axes so the bounding box aligns with the geometry.
There are many times when modeling in SketchUp where the order of operations can make your work easier or more difficult. With time and use you’ll figure them out.