It's a useful tool, but it will also report potential conflicts between two hacks that share procedures because they've been designed to work together. The TJ re-write of Laserarcsims' Pregnancy For All was intended to work as a plug-in for the Jase-adapted versions of the Jenflower Teen WooHoo mod, but it generates three different possible conflict reports with it when you run this tool.
It also reported a number of possible conflicts between mods that have been quietly sitting together in my dowloads folder for months or years without affecting gameplay. So if you have some unexplained glitching it might help to pin down where it's coming from, but you shouldn't assume that everything it reports should be removed.