Nega-Scott is treated as Scott's Evil Twin rather than his Enemy Without. Every difference in Nega-Scott's continuity in the game comes as a result of this.
Being rejected as an evil twin rather than accepted as a manifestation of Scott's own flaws in the first place accounts for Nega-Scott taking on stock supervillain powers and tropes, such as necromancy and evil laughter, along with being a proper boss battle. Scott denying a part of himself so badly (treating it as an entirely separate being) empowers Nega-Scott far beyond the limits seen in the comic.
Nega-Scott's ending has him sending all the other fighters to the salt mines before going to bed, a childish rendition of what it means to Take Over the World. Overwhelming Scott and his orbit much like a rejected Shadow from the Persona series, he represents Scott's flaws consuming him because he can't face them.
Scott's ending sees Ramona gone, with him dating Kim, Knives, and Envy all at once, and he's hinted to not be as happy as he thinks. In Scott's story, he defeats Nega-Scott in the boss battle instead of accepting Nega-Scott as his problems made manifest; which means unlike the comic, he doesn't learn from his mistakes and keeps making them over and over. In marked contrast, Ramona defeating Nega-Scott (by being the first player) directly leads to her ending where she and Scott become an official couple, because that means she accepts his mistakes and flaws unconditionally.
Why does Toronto, Canada look like an island in the overworld map? Todd Ingram punched a hole in the moon, causing 30 pages worth of tidal waves and explosions. Think about that. This also explains why there are pipes built to expunge water into the ocean.
