Ride: "The 90 minute wait ride".
This ride loads 300 people an hour. There are 449 people in the line. It is 11AM.
Since we don't know the dynamics of the park this day, let's assume the line for the ride is always full. The park is open from 9AM to 9PM. 3600 will ride this ride today (300 people/hour * 12 hours).
Example 1: You get in Stand By Line at 11AM. There are 449 people ahead of you. 600 people already rode the ride today (9AM - 11AM). You wait 90 minutes and ride the ride. By the time you get on the ride (12:30PM), 950 people will have ridden. Between 12:30PM and 9PM, 2550 more people will ride after you. Total: 3600 (600 before 11AM + 449 in line + you + 2550 after you)
Example 2: You get a FastPass. It instructs you to arrive back no earlier than 90 minutes. At 12:30PM, you get in the FastPass line. There is no one else ahead of you in the FastPass line. The 449 people in line ahead of you get to ride the ride, and then it is your turn. Between 12:30PM and 9PM (8.5 hours), 2550 (300 * 8.5) more people will ride after you. Total: 3600 (600 before 11AM + 449 in line + you + 2550 after you)
Example 3: You get a FastPass. You come back at 1:30PM, which is at the end of your window. There is no one else ahead of you in the FastPass line. The 449 people originally in line ahead of you ride the ride, plus an additional 300 (1 hour window * 300) people who got in line between the start and end of your window. Between 1:30PM and 9PM (7.5 hours), 2250 (300 * 7.5) will ride the ride. Total: 3600 (600 before 11AM + 449 in line when you get your FastPass + another 300 during your window + you + 2250 after you)
Example 4: You get a FastPass. You come back at 5PM, which is after your window. There is no one else ahead of you in the FastPass line. The 449 people originally in line ahead of you ride the ride, plus an additional 1350 (4.5 hours * 300) people who got in line between the start your window and 5PM. Between 5PM and 9PM (4 hours), 1200 (300 * 4) will ride the ride. Total: 3600 (600 before 11AM + 449 in line when you get your FastPass + another 1350 during your window + you + 1200 after you)
Basically, by coming after your window, you are letting more people "virtually" in front if you. It's like standing in line, and when it's your turn, standing aside and letting more people ride (maybe because you are waiting for someone farther back in the line). I see no problem with coming after the end of your window.