I have the Z5 Compact with flip cover. My flip cover came with a suitable insert for the dock so that you can put the smartphone in with the flip cover. The docking also comes with a few interchangeable inserts. Unfortunately, I don't know if one of them is for the Z5 with flip cover. Sony customer service can probably help you better...

The lowest approx. 5 mm of the mobile phone is inserted into the docking station. If the cover is also in this area (which is probably the case), the cover must be removed so that the phone fits into the docking station. So the answer is most likely no.