You will need to replace the encoder with one with a longer shaft, as the encoder knob goes above the top of the metal case, rather than being recessed into it, as it is with the acrylic case.
I think (someone correct me if I’m wrong here) you can use the item listed in the Ambika mainboard BOM.
The newer kids all have longer encoders. The old one used to have short ones. You can easily see it. The encoder needs to have about the same hight as the pots.