Just had the first test run with a buildtak print surface. I had the exact same problem, so I searched for a solution here in the forum.
The nozzle making holes into the buildtak additional surface is not really ideal. what I would love to see is an option within the menu (using an ultimaker s3) to choose between different print-surfaces. this way you could choose maybe a glass (standard), buildtak, others... after that the printer knows on which surface he prints on, so that the starting routine could be the right one depending on the surface material.