If chef considers following his idea to the letter more important than the result then you're in a tough position. If you're baking the cake, pouring on a custard base and baking again, the cake is being overbaked. It's also going to leach moisture from the custard base changing the texture of both the cake and the resulting custard. If chef refuses to budge on this, maybe use Jaymes' idea of the custard cake, bake them in individual serving dishes and cover the top of each ramekin with a premade sugar disc before serving. The custard will be on the bottom but they'll be baked together since that seems to be the party trick he wants. I don't know the situation you're working in or I'd suggest diplomatically telling chef that people have to eat my dessert so it's more important to me that they enjoy eating it than be amazed because they were baked together.
Without being disrespectful to my chef, I would jusy say that everyone has painted a prett good picture of his character and knowlege. I believe he saw this dessert at a previus restaurant that he (not I) worked at and wants to recreate it, without a recipe of course.
He was adamant of the two layers being baked together, and I completely agree that if the cake is solid enough to support the brulee mix, it's going to overcook. I think Jaymes' idea would look elegant on the plate, especially with a pretty sugar disk on top. That will have to wait for one of my dinner parties though..