The only people that are really stuck with a ride/sag decision will be single riders who have no support vehicle or team to move them up the route to another start location or sag. Some charters have limited sag service. But seeing this as an unusual day, may schedule special transportation for their paying customers to the meeting town who want to cut the miles or sag the entire day.
One year, a family medical problem required me to drive out to RAGBRAI and meet my team on day 2. I had no problem finding one or more team members who wanted to sag the entire day or split the ride by parking the car in the meeting town. I see RAGBRAI now allows riders who are not part of an official team to bring a support vehicle. This may have unintended consequences of increasing cars and traffic. The 100 mile day may prompt individual riders who otherwise would not consider bringing a car to create an informal car pool. This forum or other social media is an ideal means to make those connections.
The basic mileage to Charles City is around 80. RAGBRAI will need to adjust the route north and south to add 20 miles. Once the route is posted in a few weeks, free apps like Ride with GPS will show you bike friendly routes to bypass portions of the route and cut miles. The Heatmap function of these apps show you what roads are frequently used by locals and point you to a preferred route. I would not be surprised to see a publicly posted route of this type to appear on RWGPS.
As to your question on how it may hurt through towns, just considering the above options riders may use to shorten or bypass the ride it is going to cut customers and limit their stays. The roadside operations with quick turnaround may be the winners.
RAGBRAI has now given people plenty of notice of what’s coming. Riders can train up for the century or if physical limitations or children prevents them from riding 100 miles, they consider other options. As riders roll into Charles City, no one is going to know and few will care if the riders rode all of the mandatory 100 miles. As the past 2 years have shown, mandates have their limitations and unintended consequences.