You are absolutely right. There are several solutions. One is to use several inner covers/crown boards, stacked on top of each other until the knobs clear the roof. Another is to put a very shallow box or two (often called an Imirie shim) on top of the inner cover but under the roof. Here is a very thin one:
A third (least desirable) is not to worry about the skew, and when you come to harvest, just prop the lid up during the actual process.
You could also nail a couple of wood blocks inside your roof to lift it up, if it is the telescoping type. If you have a migratory cover, that will definitely not work.