I believe those twilight are added AFTER all moving operations.
Movement Summary
• A Shadow player places the next site card, if needed.
• Move your player marker to the next site.
• Perform "When you move from..." actions.
• Perform "When the fellowship moves..." actions.
• Perform "When you move to..." actions.
• Add twilight tokens equal to the new site's Shadow number.
• Add 3 twilight tokens if the new site is in region 2; or 6 if it is in region 3.
• Add 1 twilight token for each companion.