Is any explanation offered for the anime’s ending regarding lost bodily function?
This is explained in the bonus chapter 「その後の園子」 (Sono Ato no Sonoko, Sonoko After), published on Dengeki G's magazine ed. 2015/03.

The story talks about the everyday life of Nogi Sonoko and the heroes after the final battle. It also explains the reason why the divine tree decided to "reverse the effect".

Excerpt from the script (possible spoiler for 2nd season, heavily redacted to answer the question only):


   After the party, Sonoko went over to Tougou's house. Yuuna was probably being considerate. Today, she left them alone. The two had a lot to talk about.
 About everything that's happened so far.
 About their dear friend.
 And...
 "Have you heard the reason everyone's getting their offerings back, Sonocchi?"
 The other side of the incident.
 Sonoko smiled.

 [...]

 "The Shinju-sama... came to believe in human courage~"

 [...]

 "However the Shinju-sama came to believe in the courage of mankind. By witnessing Yu~yu's and everyone's hard work, as well as getting plenty of Vertex combat data, the hero system was updated to the next stage."

 [...]

 "Don't think negatively about the situation. The Shinju-sama believed mankind would be able to walk down the harsh path, instead of a gentle one that lead to its demise. That is why it gave back our offerings and allowed for mass-production of the system so that everyone would be able to stand and fight. Everyone will don their own flower~. Isn't that a good thing?"