When Top O' and I decided yesterday to follow the Leeds Creek Alternate, we did that because we learned it was a more scenic route. We wanted to follow another alternate today to get where we could make campsite reservations in Yellowstone National Park. In a few days, we will walk on a long alternate that goes around a fire closure.
More than a dozen alternates are documented in trail guides, and several more are mentioned in blogs and Guthook comments. They are all acceptable substitutions for the official Continental Divide Trail route. No rules say they can't be used to qualify for a thru-hike. Most hikers choose to use at least a few of them.
This is why the CDT is often called a choose-your-own-adventure trail. The official route never veers farther than 50 miles from the divide. The generally accepted practice for alternates is to also stay within that corridor.
The freedom to pick your own route allows you to find a path that best suits your interests and skills. It's also a wise practice because it encourages hikers to choose a safer route when a fire or heavy snow makes the trail dangerous.