Why German warships grew overweight

Were German ships often overweight because of their machinery?

Not chiefly. The larger problem was continuing to add equipment after a design was settled, increasing complexity and displacement.

Machinery is rejected as the main reason German warships became overweight. The larger problem was design growth after the basic design had been settled. Repeated additions increased complexity and displacement until the finished ship no longer matched the original assumptions. Controlling new requirements after the design was settled mattered more than any single machinery choice.