I really do not think 2 years of almost no training does that much. I do not know what people think missionaries are doing. They are under pretty strict rules and are hardly given time for exercise. Most people I know coming back from missions are pudgier than before. Here is a quote from an article a while back on Shaq Walker (
https://www.deseretnews.com/article/865621680/BYU-star-Shaquille-Walker-is-a-secret-no-more.html
):
"He estimates that he ran a total of 25-30 miles during the next two years. When he returned to Provo last August and resumed training, he was understandably out of shape. During his first workout with the team, he got halfway through a four-mile run before he quit and walked home."
I've heard there is a "training plan" that Eyestone advises his athletes to follow during the missions but the BYU XC and T&F distance athletes all have a good laugh about it because mission schedules are not built around your athletic goals. It is also inconvenient to run in certain places, and prospective missionaries hardly have any say in where they will go.
A recent article on Casey Clinger made it sound like he is squeezing in some maintenance running and is lucky to have a companion who wants to run. If he gets assigned a different companion who doesn't like running though, then he'll have to deal with it because one of the mission rules is you pretty much have to be within earshot/eyesight of your companion at all times except when using the restroom or taking a shower.
Even if the maturity factor is influential, a two year hiatus from consistent running definitely has unpredictable consequences. Also BYU is not the only school training returned missionaries. Elijah Armstrong (quite a talented high school runner) for BSU is just one example. And yeah I know BYU attracts prospective and returned missionaries for obvious reasons, but if there are really such glorious athletic benefits to be reaped from the two year break, then maybe other colleges can make their programs more attractive to American Fork boys and other Utah areas from where a large chunk of their team is supplied.