The "mature" rating wasn't for homosexual themes: it was for other reasons (graphic violence, nudity [both male and female], drug abuse, and other adult themes)
A heterosexual couple show affection and the movie is slapped with a PG-13 rating
Yuuko and Kenta get an M because of a heavily implied Sexy Discretion Shot of the two making love in Highschool Troperia!.
Subverted: The movie was gonna get a PG-13, but the censorship board thought that slapping it with a PG-13 rating because of the homosexual themes would be a bit over the top.
Double Subverted: But they change their minds and give it a PG-13 anyway, either due to protests from conservative groups or because the film has other content that wouldn't be appropriate for younger audiences.
Zig Zagged: The American version is rated R for its homosexual references; every other country in the world either gives it a lighter rating (mostly an equivalent to the PG-13 rating, such as Britain's 12 and 15 ratings or Canada's 14A rating) or (in the cases of many Muslim countries) bans it from being shown.
There is no homosexual subtext for the censors to get in an uproar about.
Bob and George do something explicit and the film is rated M as a result, because the scene meets the criteria for it.
Defied: The editor in charge of Highschool Troperia! forced the author to alter that scene for the volume release. Those who don't read the magazine the manga is serialized on will never know that Ichigo and Yuuko kissed.
"Oh so that's where the mature rating comes from!"
Alice rents a movie about a homosexual couple and is angry when she learns the R-rating is simply because of the homosexual relationship. She calls up her friends and discusses it.
Deconstructed: Gay rights activists and members of the Gay and Lesbian Alliance Against Defamation see the censorship of High School Troperia!'s lesbian couple as homophobic and proceed to sue the censorship board.
Reconstructed: The jury looks at the movie and rules that, even without the homosexual references, the movie would have been rated PG-13 or R for everything else.