Actually wouldn't be surprised if that was the whole point of "yaoi" omake. I mean, miss Kodama could've been just having fun with the tropes, but for whatever reason i doubt that was the case. Then again, she really likes drama, so maybe she just wanted to add another layer of the icing to the already overstacked cake. Who knows.
Btw, i really enjoyed it. Some people call it trash (or "NTR crap"), but i think it's a fun ride. Maybe too melodramatic and tad bit too long, but fun nonetheless. Solid 6.5, maybe seven if you take art into account.