I guess the joke was more related to me not being sure that the evaluation is insensitive to the order of the crop, and Juan stating (as he did a few time) that the evaluations are not sensitive due to the limits 00.-0.98 (they are hardcoded in a few places). Maybe PI is too good and we apply folkloric tricks (like truncating before integration) that are long needed ...
The short answer is: truncate at the end. If you create a single integrated image (DSLR), you can use the dark rejection mask to find the area to truncate very easily.
The second point is: do not hesitate to ask questions if you do not find the answer already. And sometime even if you do, you may get other opinions, alternate ways doing things, and so on.... PI is a living object.
-- bitli