Hi, Yes this is correct and described on the product page for OSPi. Basically, the enclosure mold we are using is quite expensive and currently we are only using one case for all three platforms. The case is tailored for the Arduino based product, which is meant to be the easy drop in replacement.
The Pi and Beagle therefore will fit and work inside this case but the ports are not tailored or cut out properly for the them. As you mentioned, you are welcome to cut your own holes in the case for access.