It actually isn’t in your pcb svg, but rather schematic where the pins don’t match. In Fritzing all three views breadboard, schematic and pcb are linked together and a change in one reflects in to the other two (and errors such as an undefined pin in one view also reflects in to the other 2).
I’m a fan of doing what works best/easiest for you 
. I’ll adjust my part to match the hole sizes and positioning in the fzz file and post that part. Then you can, if you wish, use a part instead of your current method or use your current method if that works better for you.
Peter