How to accurately calculate cross-section area of STL

I’ve managed to solve the cylinder problem by turning on ‘Reorient Difference Cells’ in the BooleanOperations filter. However, I’ve noticed a new issue with the Clip Closed Surface filter. After running the boolean difference operation between the STL and cylinder, if I use Clip Closed Surface filter, sometimes the holes aren’t completely closed. This generally seems to happen if the filter cuts through the difference area between the STL and cylinder and there are two or more areas in the result, as shown in the screenshot. Is this a bug or am I doing something wrong?