Seems like an odd place for one. The string retainer hole - I want to bean the person that did such a god awful repair job. What’s the TB opinion?
Yeah, sucks that they neglected to mention the botched string bar job. For sure contact them and let them know about your displeasure, but personally I wouldn't be too quick to write it off if you like the bass otherwise. If you aren't a perfectionist see if you can get a deep discount and then either live with it as is or fix it better. From the pictures you sent the damage is largely cosmetic so it will probably be fully functional either way. Keep in mind there was a hole for the screws
most of the way through the head stock right from the factory. Now it is just a bit deeper and wider but maple is strong stuff.
You could make a decent repair of the hole by simply drilling out the filler and gluing in a piece of maple dowel in its place, then sanding it flush, drilling a new pilot hole for the right size screw and refinishing the neck. You would still see the repair if you went looking but it would be subtle and it is on the bottom of the head stock too.
The crack looks like a stress crack caused by the string contacting the end of the neck behind the nut. Again, just cosmetic. That happened due to having the nut slots too deep (looks like some of those strings were practically resting on the fingerboard!) combined with having the string bar too low. I am actually surprised to see the crack didn't make it all the way to a screw hole as cracks around screw holes are pretty common.
Anyway, fixing all that will be made more difficult because of the chip that came out around that screw hole. A few options come to mind if you are feeling ambitious/adventurous, in rough order of least to most effort:
1. Remove all the hardware from the head stock, clean up the chip and cut and glue a piece of maple (birdseye if possible) veneer to fit the chip. Then fill, sand smooth and refinish the head stock by re-spraying a burst around the perimeter then clear the whole thing. If you made the burst a bit wider and more opaque it wouldn't be real obvious without close inspection. You should be able to preserve the original lettering that way too.
2. Remove all the hardware from the head stock, fill the chip with wood filler and sand flush, mask the sides and back of the head stock plus the entire neck and spray the head stock in a solid color of your choice. My Millennium came with a black head stock face originally but it is a trans black maple body. Black may not be your color but something else might look good. Whatever color you choose you will still need to reproduce the logos if you want it to look like it
could have been original.
3. Sand the entire head stock down to good solid wood. This would mean the area around the string bar would be thinner and thus less strong but I doubt it would give any trouble. Respray the burst and clear it, or leave it with whatever finish you prefer. You will need to reproduce the logos if you want it to look original. This should get you back to a perfect, like new, finish but is obviously a lot of work.
If it were me I would probably do option 3, including stripping the entire neck and refinishing in tung oil. That birdseye looks like a real beauty and playing that with an oiled finish would be worth the effort.
Hope it all works out!