Normally the front fork braze-ons are done with a water bottle mount. They can also be done with the rear stay mount you show, though it looks uglier. If you are making your own racks you should be able to choose the position with some care. Start backwards. Choose panniers, design rack, modify frame to carry rack dead level.
When it comes to positioning the BOs, those spool shaped ones are normally mounted on a piece of threaded rod to keep them aligned with each other. If you use the water bottle mounts they are positioned in holes, though getting them square may take some fritzing. A rack is not always a perfect mounting jig, since even a well made rack is not always bylaterally simetrical. It's a back and forth process. You design the rack. You positon and install the BOs from the rack, then you install them, then you mount the eyelets to the inserts/BOs, then you braze the rack to those. Something like that. If you are going into production you build manufacturing fixtures so that everything is interchangeable, but the fun of custom is being able to tweak everything.