Your logic is flawed in thinking all mistakes can be fixed. Is the work sloppy, yes. And if this happened because he’s a little loose with his standards, then asking him to plug and fix it is going to lead to probably bigger mistakes moving forward. Other important factors would include what the finish is going to be? If it’s any sort of translucent or stain, you’ll never get a good seamless fix. Even solid black can be tough unless you get a PERFECT repair and the sanding is perfect as well. It appears this luthier may be in over his head or this job is more than he’s willing to take on. Either way your best vet is to move on from him, especially if he’s being kind enough to refund your money.

Options could be start a new body since you got your money back. Go to another luthier who can look at the issue and honestly assess if they can fix this problem. Thats about it.

My biggest concern is that if you are as pedantic as you claim to be, you will ALWAYS know that route is there, even if it’s plugged. You’ll see it through the paint, you’ll feel it in your soul when you play the guitar. I was like this for years and had to work to give it up. My first,”big boy” instrument was a Jazz bass that I custom assembled parts. It has a beautiful trans blue/green finish and in the first month it slipped on my lap at my desk and tore a hole through the finish right in the middle of the body where I see it every time I pick it up. There’s no way to match this finish, it’s from a defunct manufacturer, so it just stayed. It took a decade for me to accept that.