I have no idea what you mean, and I can't reproduce it (if I think I got you correctly).
First off, please don't quote such a big post...
Anyways, it should be possible to pack a sixth sample number bit into the period (note) unit in the pattern data, meaning that sample numbers can be 01..3F (63 samples). Though this would require changing a whole lot of hardcoded "31 samples" code, and it would naturally cause problems normal MODs. I don't think I'm going to do that any time soon, I'm focusing on a compatible ProTracker for now.