As Grumpy said, the crack .dll file overwrites any changes made by the official patch. In addition to fixing the boat crash-to-desktop bug, there's some additional dialogue that I'd love to see (having Isaac acknowledge the completion of the Gargoyle quest, for example), and some other big fiixes.
The game is still playable (with the major workaround in the console for the Leopold bug, of course) without the patch, but it would be nifty to have both the convenience of the NO-CD crack and the latest patch!
Thanks to the amazing folks doing that work, by the way!
Cheers,
-M