The sunken dot is because they drilled the hole for it too deep at the factory. You’d be right to ask for a replacement neck unless you really want to have a go at repairing it yourself (but then you risk not getting a replacement if that doesn’t go well).
Measure the dot inlay circumference. It’s probably 6mm but worth checking. You can get plastic or abalone replacement dot sets on Amazon or eBay as well as luthier suppliers.
You could go for fancier dot inlays and replace them all, or just pick a set that looks the same and replace just that dot. I’d drill the old dot out (use a hand drill), and fill the hole with wood filler until there’s just enough depth to accommodate the new dot. As a minimum it will want to be slightly proud in the centre and level at the sides, but slightly proud all round is OK. Sparingly glue it in place with either epoxy or superglue, but avoid getting excess glue squeezing out round the sides.
Once the glue’s hardened, then its a process of filing and sanding the dot flush with the fingerboard. It’s a lot easier with no frets in place, but I’d use a flat needle file to start with running across the neck, then use sandpaper running along the neck with the wood grain. Mask off the frets first with tape to prevent scratching them. I’d start with P240 and work up to P2000 to remove any scratch marks. If you have any Micromesh pads or cloth, then you can carry on with those for an even shinier finish if necessary. Try and get the same shine level as the others (though I often have a go at polishing them up a bit more).
Looking forward to seeing the build progress, it sounds very interesting indeed!
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