To expand on this, the last volume of the comics came out just a few weeks before the movie. There was an ending shot where Scott gets with Knives in the end, which is what the last act was building towards. But as soon as it was learned that Scott would be with Ramona after all, they did some last-minute reshoots to change literally the last few minutes of the movie and had Scott get back together with Ramona and with Knives’ blessing.

Presumably they at least learned this a bit before the comic was actually available to purchase, because that is way too short notice to do retakes otherwise.