This is a close call in my opinion but you have a ton of options. I had a pair with similar issues and talked to Alden. They offered to re-dye the shoes. I'm going to wait for recrafting and have it taken care of. Here are your options:
1. Keep as-is and wait for recrafting. These spots will not look as significant with a bit of wear. Maybe they will fade into patina and you won't need a re-dye.
2. Ask TSM for a discount. Some people on here will discourage this, but IMO these should be seconds and should be priced accordingly.
3. TSM could potentially fix this. I had a similar issue with TSM and they offered to take the shoe from me to fix the issue in house. Not sure what they do but could be worth a shot.
4. Return em - just be sure you dont crease em