Perhaps almost inevitable with burl unless its a really high priced job. Seems to me that a lot of veneers would get thrown away if they insisted on every one being perfect. I admire anyone who can work with it, its way beyond my skill set.
Still, that does look nice.
One thing I did with my tru oil instrument, where I was filling over an inlaid headstock veneer, was to build it up with repeated layers of tru oil sealer filler, literally dripped on thick and left to cure, until I was eventually able to sand it flush. Some layers were so thick they wrinkled up when curing, but now its sanded and polished I can't tell. Might be worth trying if you haven't filled your drop outs another way.