To the OP.....the shop did exactly what you wanted them to do.
I wax my own board several times per year and that's what the wax is like after you melt it on/into the base if you use a lot of wax. When it dries, it can look like a thick layer and it will be uneven unless you try really hard to make it smooth which is pointless since you'll be scrapping it off soon anyway.
Don't worry, plenty of wax got into the base and what you are seeing is the excess wax that is perfect to protect your base and keep it sealed over the summer.
I suggest you buy yourself a scrapping tool and watch some videos about how to wax your board. When the snow starts to fall next winter, scrape that wax off yourself and you'll be ready to roll.
To the other person that asked about storing their boards....melt the wax onto the board evenly and leave all the wax on there for the summer. Then scrape off next year when you are ready to ride.
The joys of customer service. They tell you what they want, you give it to them exactly, and they get upset and spout off on the internet anyway.
Don't be tough on the guy. He just didn't know. . .that's why he asked. I remember having that done for the first time at the end of last season, getting the board back and shaking my head as it dawned on me. . .shit, I could've done that!