Viewport renders at the game's resolution and stretches that render to the window's size, while 2D renders the game at the window's resolution, so if you make the window twice as big, the game will render 4 times as many pixels.

The defects you're seeing are linked to texture filtering and happen in every engine. There are some ways to avoid them, like removing the filter option on the texture, or by leaving a bleeding area of a few pixels around every tile on the tileset's image.